Mercurial > repos > galaxyp > msi_qualitycontrol

annotate msi_qualitycontrol.xml @ 14:7c7c39b9ec4a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
author galaxyp
date Tue, 24 Jul 2018 04:53:25 -0400
parents 88e12d270e35
children 2d69460669ae
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1 <tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.10.0.5">
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
2 <description>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
3 mass spectrometry imaging QC
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
4 </description>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
5 <requirements>
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
7 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
8 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
9 <requirement type="package" version="2.2.1">r-gridextra</requirement>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
10 <requirement type="package" version="2.23_15">r-kernsmooth</requirement>
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
11 <requirement type="package" version="0.5.0">r-scales</requirement>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
12 </requirements>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
13 <command detect_errors="exit_code">
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
14 <![CDATA[
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
15 #if $infile.ext == 'imzml'
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
16 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
17 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
18 #elif $infile.ext == 'analyze75'
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
19 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
20 ln -s '${infile.extra_files_path}/img' infile.img &&
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
21 ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
22 #else
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
23 ln -s '$infile' infile.RData &&
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
24 #end if
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
25 cat '${cardinal_qualitycontrol_script}' &&
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
26 Rscript '${cardinal_qualitycontrol_script}'
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
27 ]]>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
28 </command>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
29 <configfiles>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
30 <configfile name="cardinal_qualitycontrol_script"><![CDATA[
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
31
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
32 ################################# load libraries and read file #################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
33
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
34 library(Cardinal)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
35 library(ggplot2)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
36 library(RColorBrewer)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
37 library(gridExtra)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
38 library(KernSmooth)
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
39 library(scales)
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
40
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
41
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
42 #if $infile.ext == 'imzml'
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
43 #if str($processed_cond.processed_file) == "processed":
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
44 msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
45 #else
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
46 msidata <- readImzML('infile')
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
47 #end if
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
48 #elif $infile.ext == 'analyze75'
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
49 msidata = readAnalyze('infile')
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
50 #else
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
51 load('infile.RData')
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
52 #end if
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
53
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
54 ## create full matrix to make processed imzML files compatible with segmentation and other steps
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
55 iData(msidata) <- iData(msidata)[]
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
56
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
57 ## remove duplicated coordinates
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
58 print(paste0(sum(duplicated(coord(msidata))), " duplicated coordinates were removed"))
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
59 msidata <- msidata[,!duplicated(coord(msidata))]
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
60
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
61 ## optional annotation from tabular file to obtain pixel groups (otherwise all pixels are considered to be one sample)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
62
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
63 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
64
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
65 ## read and extract x,y,annotation information
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
66 input_tabular = read.delim("$tabular_annotation.annotation_file", header = TRUE, stringsAsFactors = FALSE)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
67 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
68 annotation_name = colnames(annotation_input)[3] ##extract header for annotations to later export tabular with same name
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
69 colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation"
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
70
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
71 ## merge with coordinate information of msidata
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
72 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
73 colnames(msidata_coordinates)[3] = "pixel_index"
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
74 merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
75 merged_annotation[is.na(merged_annotation)] = "NA"
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
76 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
77 msidata\$annotation = as.factor(merged_annotation[,4])
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
78
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
79 #end if
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
80
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
81 ###################################### file properties in numbers ######################
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
82
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
83 ## Number of features (m/z)
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
84 maxfeatures = length(features(msidata))
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
85 ## Range m/z
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
86 minmz = round(min(mz(msidata)), digits=2)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
87 maxmz = round(max(mz(msidata)), digits=2)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
88 ## Number of spectra (pixels)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
89 pixelcount = length(pixels(msidata))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
90 ## Range x coordinates
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
91 minimumx = min(coord(msidata)[,1])
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
92 maximumx = max(coord(msidata)[,1])
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
93 ## Range y coordinates
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
94 minimumy = min(coord(msidata)[,2])
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
95 maximumy = max(coord(msidata)[,2])
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
96 ## Range of intensities
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
97 minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2)
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
98 maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2)
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
99 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
100 ## Number of intensities > 0
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
101 npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
102 ## Spectra multiplied with m/z (potential number of peaks)
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
103 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
104 ## Percentage of intensities > 0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
105 percpeaks = round(npeaks/numpeaks*100, digits=2)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
106 ## Number of empty TICs
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
107 TICs = colSums(spectra(msidata)[], na.rm=TRUE)
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
108 NumemptyTIC = sum(TICs == 0)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
109 ## Median TIC
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
110 medTIC = round(median(TICs), digits=2)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
111 ## Median peaks per spectrum
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
112 medpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE), na.rm=TRUE)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
113 print(cor(TICs,colSums(spectra(msidata)[]>0), method="pearson"))
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
114
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
115 ## Processing informations
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
116 processinginfo = processingData(msidata)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
117 centroidedinfo = processinginfo@centroided
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
118
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
119 ## if TRUE write processinginfo if FALSE write FALSE
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
120
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
121 ## normalization
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
122 if (length(processinginfo@normalization) == 0) {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
123 normalizationinfo='FALSE'
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
124 } else {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
125 normalizationinfo=processinginfo@normalization
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
126 }
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
127 ## smoothing
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
128 if (length(processinginfo@smoothing) == 0) {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
129 smoothinginfo='FALSE'
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
130 } else {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
131 smoothinginfo=processinginfo@smoothing
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
132 }
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
133 ## baseline
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
134 if (length(processinginfo@baselineReduction) == 0) {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
135 baselinereductioninfo='FALSE'
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
136 } else {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
137 baselinereductioninfo=processinginfo@baselineReduction
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
138 }
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
139 ## peak picking
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
140 if (length(processinginfo@peakPicking) == 0) {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
141 peakpickinginfo='FALSE'
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
142 } else {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
143 peakpickinginfo=processinginfo@peakPicking
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
144 }
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
145
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
146 ############## Read and filter tabular file with m/z ###########################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
147
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
148 ### reading calibrant file:
4
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
149
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
150 #if $calibrant_file:
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
151
4
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
152 calibrant_list = read.delim("$calibrant_file", header = FALSE, na.strings=c("","NA"), stringsAsFactors = FALSE)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
153 if (ncol(calibrant_list) == 1)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
154 {calibrant_list = cbind(calibrant_list, calibrant_list)} ## if there is just one column dublicate it to have a names column
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
155
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
156 ### calculate how many input calibrant m/z are valid:
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
157
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
158 inputcalibrants = calibrant_list[calibrant_list[,1]>minmz & calibrant_list[,1]<maxmz,]
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
159 number_calibrants_in = length(calibrant_list[,1])
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
160 number_calibrants_valid = length(inputcalibrants[,1])
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
161
4
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
162 #else
5
ac786240ef07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
galaxyp
parents: 4
diff changeset
163
ac786240ef07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
galaxyp
parents: 4
diff changeset
164 inputcalibrants = as.data.frame(matrix(, nrow = 0, ncol = 2))
4
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
165 number_calibrants_in = 0
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
166 number_calibrants_valid = 0
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
167
4
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
168 #end if
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
169
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
170 ## rename input dataframe and extract m/z
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
171 colnames(inputcalibrants) = c("m/z", "name")
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
172 inputcalibrantmasses = inputcalibrants[,1]
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
173
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
174
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
175 ######################################## PDF #############################################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
176 ##########################################################################################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
177 ##########################################################################################
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
178
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
179 pdf("qualitycontrol.pdf", fonts = "Times", pointsize = 12)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
180 plot(0,type='n',axes=FALSE,ann=FALSE)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
181
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
182 ## if no filename is given, name of file in Galaxy history is used
5
ac786240ef07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
galaxyp
parents: 4
diff changeset
183
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
184 #if not $filename:
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
185 #set $filename = $infile.display_name
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
186 #end if
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
187
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
188 title(main=paste("$filename"))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
189
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
190 ################# I) file properties in numbers ################################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
191 ################################################################################
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
192 print("properties in numbers")
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
193
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
194 properties = c("Number of m/z features",
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
195 "Range of m/z values",
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
196 "Number of pixels",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
197 "Range of x coordinates",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
198 "Range of y coordinates",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
199 "Range of intensities",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
200 "Median of intensities",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
201 "Intensities > 0",
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
202 "Number of empty spectra",
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
203 "Median TIC",
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
204 "Median # peaks per spectrum",
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
205 "Normalization",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
206 "Smoothing",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
207 "Baseline reduction",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
208 "Peak picking",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
209 "Centroided",
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
210 paste0("calibrants (#valid/#input) in \n", "$calibrant_file.display_name"))
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
211
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
212 values = c(paste0(maxfeatures),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
213 paste0(minmz, " - ", maxmz),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
214 paste0(pixelcount),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
215 paste0(minimumx, " - ", maximumx),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
216 paste0(minimumy, " - ", maximumy),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
217 paste0(minint, " - ", maxint),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
218 paste0(medint),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
219 paste0(percpeaks, " %"),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
220 paste0(NumemptyTIC),
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
221 paste0(medTIC),
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
222 paste0(medpeaks),
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
223 paste0(normalizationinfo),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
224 paste0(smoothinginfo),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
225 paste0(baselinereductioninfo),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
226 paste0(peakpickinginfo),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
227 paste0(centroidedinfo),
4
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
228 paste0(number_calibrants_valid, " / ", number_calibrants_in))
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
229
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
230 property_df = data.frame(properties, values)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
231
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
232 grid.table(property_df, rows= NULL)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
233
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
234 ####################### II) x-y images #######################################
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
235 ##############################################################################
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
236 print("x-y images")
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
237
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
238 ## only do plots for file with intensity peaks
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
239 if (npeaks > 0){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
240 ## function for density plots
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
241 plot_colorByDensity = function(x1,x2,
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
242 ylim=c(min(x2),max(x2)),
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
243 xlim=c(min(x1),max(x1)),
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
244 xlab="",ylab="",main=""){
4
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
245 df = data.frame(x1,x2)
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
246 x = densCols(x1,x2, colramp=colorRampPalette(c("black", "white")))
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
247 df\$dens = col2rgb(x)[1,] + 1L
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
248 cols = colorRampPalette(c("#000099", "#00FEFF", "#45FE4F","#FCFF00", "#FF9400", "#FF3100"))(256)
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
249 df\$col = cols[df\$dens]
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
250 plot(x2~x1, data=df[order(df\$dens),], ylim=ylim,xlim=xlim,pch=20,col=col,
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
251 cex=1,xlab=xlab,ylab=ylab,las=1, main=main)}
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
252
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
253 ## start list for optional spectrum values output
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
254 spectrum_list = list()
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
255 list_count = 1
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
256
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
257 ################### 0) overview for combined data ###########################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
258
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
259 ### only for previously combined data, same plot as in combine QC pdf
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
260
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
261 if (!is.null(levels(msidata\$annotation))){
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
262 number_combined = length(levels(msidata\$annotation))
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
263
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
264 ## the more annotation groups a file has the smaller will be the legend
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
265 if (number_combined<20){
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
266 legend_size = 10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
267 cex_boxplot = 1
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
268 }else if (number_combined>20 && number_combined<40){
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
269 legend_size = 9
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
270 cex_boxplot = 0.8
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
271 }else if (number_combined>40 && number_combined<60){
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
272 legend_size = 8
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
273 cex_boxplot = 0.6
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
274 }else if (number_combined>60 && number_combined<100){
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
275 legend_size = 7
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
276 cex_boxplot = 0.5
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
277 }else{
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
278 legend_size = 6
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
279 cex_boxplot = 0.3
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
280 }
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
281
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
282 position_df = cbind(coord(msidata)[,1:2], msidata\$annotation)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
283 colnames(position_df)[3] = annotation_name
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
284
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
285 ## append list for optional tabular output with spectrum values
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
286 spectrum_list[[list_count]] = position_df
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
287 list_count = list_count+1
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
288
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
289 colnames(position_df)[3] = "Annotation"
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
290 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=Annotation))+
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
291 geom_tile() +
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
292 coord_fixed()+
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
293 ggtitle("Spatial orientation of combined data")+
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
294 theme_bw()+
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
295 theme(plot.title = element_text(hjust = 0.5))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
296 theme(text=element_text(family="ArialMT", face="bold", size=12))+
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
297 theme(legend.position="bottom",legend.direction="vertical")+
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
298 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
299 guides(fill=guide_legend(ncol=5,byrow=TRUE))
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
300
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
301 print(combine_plot)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
302
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
303 ### order pixels according to annotation - this gives a new pixel/spectra index order according to the annotation groups
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
304 pixel_name_df = data.frame(pixels(msidata), msidata\$annotation)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
305 colnames(pixel_name_df) = c("pixel_number", "pixel_name")
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
306
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
307 pixel_name_df_ordered = pixel_name_df[order(pixel_name_df\$pixel_name),]
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
308 pixel_name_df_ordered\$annotated_order = 1:ncol(msidata)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
309 last_pixel = aggregate(annotated_order~pixel_name, data = pixel_name_df_ordered, max)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
310
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
311 pixel_vector = last_pixel[,2]
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
312 abline_vector = pixel_vector[1:number_combined-1]
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
313 print(abline_vector)
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
314 }
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
315
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
316 ################### 1) Pixel order image ###################################
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
317
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
318 pixelnumber = 1:pixelcount
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
319 pixelxyarray=cbind(coord(msidata)[,1:2],pixelnumber)
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
320 gg_title = "Pixel order"
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
321
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
322 ## order pixels according to annotation groups if annotations are provided
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
323 if (!is.null(levels(msidata\$annotation))){
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
324 pixelxyarray = pixelxyarray[match(pixel_name_df_ordered\$pixel_number, pixelxyarray\$pixelnumber),]
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
325 pixelxyarray\$pixelnumber = 1:ncol(msidata)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
326 gg_title = "Pixel ordered for annotation groups"
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
327 }
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
328
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
329 print(ggplot(pixelxyarray, aes(x=x, y=y, fill=pixelnumber))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
330 geom_tile() + coord_fixed()+
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
331 ggtitle(gg_title) + theme_bw()+
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
332 theme(plot.title = element_text(hjust = 0.5))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
333 theme(text=element_text(family="ArialMT", face="bold", size=12))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
334 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"),
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
335 space = "Lab", na.value = "black", name = "Pixel\nnumber"))
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
336
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
337 ################ 2) Number of calibrants per spectrum ######################
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
338
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
339 ## matrix with calibrants in columns and in rows if there is peak intensity in range or not
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
340 pixelmatrix = matrix(ncol=ncol(msidata), nrow = 0)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
341
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
342 ## plot only possible when there is at least one valid calibrant
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
343 if (length(inputcalibrantmasses) != 0){
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
344
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
345 ## calculate plusminus values in m/z for each calibrant
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
346 plusminusvalues = rep($plusminus_ppm/1000000, length(inputcalibrantmasses))*inputcalibrantmasses
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
347
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
348 ## filter for m/z window of each calibrant and calculate if sum of peak intensities > 0
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
349
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
350 for (mass in 1:length(inputcalibrantmasses)){
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
351
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
352 filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],]
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
353
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
354 if (nrow(filtered_data) > 1 & sum(spectra(filtered_data)[],na.rm=TRUE) > 0){
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
355
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
356 ## intensity of all m/z > 0
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
357 intensity_sum = colSums(spectra(filtered_data)[], na.rm=TRUE) > 0
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
358
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
359 }else if(nrow(filtered_data) == 1 & sum(spectra(filtered_data)[], na.rm=TRUE) > 0){
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
360
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
361 ## intensity of only m/z > 0
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
362 intensity_sum = spectra(filtered_data)[] > 0
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
363
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
364 }else{
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
365
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
366 intensity_sum = rep(FALSE, ncol(filtered_data))}
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
367
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
368 ## for each pixel add sum of intensities > 0 in the given m/z range
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
369 pixelmatrix = rbind(pixelmatrix, intensity_sum)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
370 }
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
371
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
372 ## for each pixel count TRUE (each calibrant m/z range with intensity > 0 is TRUE)
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
373 countvector= as.factor(colSums(pixelmatrix, na.rm=TRUE))
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
374 countdf= cbind(coord(msidata)[,1:2], countvector) ## add pixel coordinates to counts
4
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
375 mycolours = c("black","grey", "darkblue", "blue", "green" , "red", "yellow", "magenta", "olivedrab1", "lightseagreen")
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
376
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
377 print(ggplot(countdf, aes(x=x, y=y, fill=countvector))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
378 geom_tile() + coord_fixed() +
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
379 ggtitle(paste0("Number of calibrants per pixel (±",$plusminus_ppm, " ppm)")) +
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
380 theme_bw() +
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
381 theme(plot.title = element_text(hjust = 0.5))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
382 theme(text=element_text(family="ArialMT", face="bold", size=12))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
383 scale_fill_manual(values = mycolours[1:length(countvector)],
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
384 na.value = "black", name = "# calibrants"))
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
385
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
386 ## append list for optional tabular output with spectrum values
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
387 colnames(countdf)[3] = "Number of Calibrants"
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
388 spectrum_list[[list_count]] = countdf
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
389 list_count = list_count+1
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
390
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
391 }else{print("2) The inputcalibrant m/z were not provided or outside the m/z range")}
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
392
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
393 ########################## 3) fold change image ###########################
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
394
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
395 #if $calibrantratio:
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
396 #for $foldchanges in $calibrantratio:
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
397 mass1 = $foldchanges.mass1
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
398 mass2 = $foldchanges.mass2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
399 distance = $foldchanges.distance
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
400
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
401 ### if user did not write a label use input m/z as label
3
f6aa0cff777c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
diff changeset
402 #if not str($foldchanges.filenameratioplot).strip():
f6aa0cff777c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
diff changeset
403 #set $label = "Fold change %s Da / %s Da" % ($foldchanges.mass1, $foldchanges.mass2)
f6aa0cff777c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
diff changeset
404 #else:
f6aa0cff777c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
diff changeset
405 #set $label = $foldchanges.filenameratioplot
f6aa0cff777c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
diff changeset
406 #end if
f6aa0cff777c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
diff changeset
407
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
408 ### filter msidata for given m/z range (for both input m/z)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
409 filtered_data1 = msidata[mz(msidata) >= mass1-distance & mz(msidata) <= mass1+distance,]
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
410 filtered_data2 = msidata[mz(msidata) >= mass2-distance & mz(msidata) <= mass2+distance,]
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
411
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
412 ### find m/z in the two given ranges with the highest mean intensity
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
413 ### this two m/z will be used to calculate the fold change (red line in plot)
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
414 maxmassrow1 = rowMeans(spectra(filtered_data1), na.rm=TRUE)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
415 maxmass1 = mz(filtered_data1)[which.max(maxmassrow1)]
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
416 maxmassrow2 = rowMeans(spectra(filtered_data2), na.rm=TRUE)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
417 maxmass2 = mz(filtered_data2)[which.max(maxmassrow2)]
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
418
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
419 ### plot legend: chosen value in blue, distance in blue, max m/z in red
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
420 ### m/z range for each plot (fixed range of 5 Da)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
421 ### xlim does not work because it does not adjust for the max. intensities within the range
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
422 mzdown1 = features(msidata, mz = mass1-2)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
423 mzup1 = features(msidata, mz = mass1+3)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
424 mzdown2 = features(msidata, mz = mass2-2)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
425 mzup2 = features(msidata, mz = mass2+3)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
426
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
427 ### plot for first m/z
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
428 par(mfrow=c(2,1), oma=c(0,0,2,0))
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
429 plot(msidata[mzdown1:mzup1,], pixel = 1:pixelcount, main=paste0("average spectrum ", mass1, " Da"))
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
430 abline(v=c(mass1-distance, mass1, mass1+distance), col="blue",lty=c(3,6,3))
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
431 abline(v=maxmass1, col="red", lty=5)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
432
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
433 ### plot for second m/z
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
434 plot(msidata[mzdown2:mzup2,], pixel = 1:pixelcount, main= paste0("average spectrum ", mass2, " Da"))
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
435 abline(v=c(mass2-distance, mass2, mass2+distance), col="blue", lty=c(3,6,3))
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
436 abline(v=maxmass2, col="red", lty=5)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
437 title("Control of fold change plot", outer=TRUE)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
438
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
439 ### filter spectra for max m/z to have two vectors, which can be divided
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
440 ### plot spatial distribution of fold change
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
441 ### only possible when there are intensities > 0 in both given m/z ranges
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
442
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
443 if (length(maxmass1)>0&length(maxmass2)>0){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
444 mass1vector = spectra(msidata)[features(msidata, mz = maxmass1),]
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
445 mass2vector = spectra(msidata)[features(msidata, mz = maxmass2),]
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
446 foldchange= log2(mass1vector/mass2vector)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
447 fcmatrix = cbind(foldchange, coord(msidata)[,1:2])
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
448
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
449 print(ggplot(fcmatrix, aes(x=x, y=y, fill=foldchange), colour=colo)+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
450 geom_tile() + coord_fixed()+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
451 ggtitle("$label")+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
452 theme_bw()+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
453 theme(plot.title = element_text(hjust = 0.5))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
454 theme(text=element_text(family="ArialMT", face="bold", size=12))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
455 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
456 ,space = "Lab", na.value = "black", name ="FC"))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
457 }else{
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
458 plot(0,type='n',axes=FALSE,ann=FALSE)
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
459 title(main=paste("At least one m/z range did not contain any intensity > 0,\n therefore no foldchange plot could be drawn"))}
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
460
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
461 #end for
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
462 #end if
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
463
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
464 #################### 4) m/z heatmaps #######################################
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
465
3
f6aa0cff777c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
diff changeset
466 par(mfrow=c(1,1), mar=c(5.1, 4.1, 4.1, 2.1), mgp=c(3, 1, 0), las=0)
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
467 if (length(inputcalibrants[,1]) != 0){
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
468 for (mass in 1:length(inputcalibrants[,1])){
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
469
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
470
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
471 image(msidata, mz=inputcalibrants[,1][mass], plusminus=plusminusvalues[mass],
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
472 main= paste0(inputcalibrants[,2][mass], ": ", round(inputcalibrants[,1][mass], digits = 2)," (±",$plusminus_ppm, " ppm)"),
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
473 contrast.enhance = "histogram", ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy))
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
474 }
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
475 } else {print("4) The input peptide and calibrant m/z were not provided or outside the m/z range")}
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
476
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
477 #################### 5) Number of peaks per pixel - image ##################
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
478
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
479 ## here every intensity value > 0 counts as pixel
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
480 peaksperpixel = colSums(spectra(msidata)[]> 0, na.rm=TRUE)
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
481 peakscoordarray=cbind(coord(msidata)[,1:2], peaksperpixel)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
482
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
483 print(ggplot(peakscoordarray, aes(x=x, y=y, fill=peaksperpixel), colour=colo)+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
484 geom_tile() + coord_fixed() +
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
485 ggtitle("Number of peaks per spectrum")+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
486 theme_bw() +
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
487 theme(plot.title = element_text(hjust = 0.5))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
488 theme(text=element_text(family="ArialMT", face="bold", size=12))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
489 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
490 ,space = "Lab", na.value = "black", name = "# peaks"))
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
491
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
492 ## append list for optional tabular output with spectrum values
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
493 colnames(peakscoordarray)[3] = "Number of Peaks"
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
494 spectrum_list[[list_count]] = peakscoordarray
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
495 list_count = list_count+1
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
496
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
497 ############################### 6) TIC image ###############################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
498
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
499 TICcoordarray=cbind(coord(msidata)[,1:2], TICs)
4
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
500 colo = colorRampPalette(
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
501 c("blue", "cyan", "green", "yellow","red"))
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
502 print(ggplot(TICcoordarray, aes(x=x, y=y, fill=TICs), colour=colo)+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
503 geom_tile() + coord_fixed() +
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
504 ggtitle("Total Ion Chromatogram")+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
505 theme_bw() +
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
506 theme(plot.title = element_text(hjust = 0.5))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
507 theme(text=element_text(family="ArialMT", face="bold", size=12))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
508 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
509 ,space = "Lab", na.value = "black", name = "TIC"))
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
510
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
511 ## append list for optional tabular output with spectrum values
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
512 colnames(TICcoordarray)[3] = "TIC per spectrum"
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
513 spectrum_list[[list_count]] = TICcoordarray
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
514 list_count = list_count+1
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
515
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
516 ############################### 7) Most abundant m/z image #################
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
517
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
518 highestmz = apply(spectra(msidata)[],2,which.max)
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
519 highestmz_matrix = cbind(coord(msidata)[,1:2],mz(msidata)[highestmz])
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
520 colnames(highestmz_matrix)[3] = "highestmzinDa"
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
521
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
522 print(ggplot(highestmz_matrix, aes(x=x, y=y, fill=highestmzinDa))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
523 geom_tile() + coord_fixed() +
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
524 ggtitle("Most abundant m/z in each spectrum")+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
525 theme_bw() +
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
526 theme(plot.title = element_text(hjust = 0.5))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
527 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"), space = "Lab", na.value = "black", name = "m/z",
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
528 limits=c(min(highestmz_matrix\$highestmzinDa), max(highestmz_matrix\$highestmzinDa)))+
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
529 theme(text=element_text(family="ArialMT", face="bold", size=12)))
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
530
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
531 ## append list for optional tabular output with spectrum values
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
532 colnames(highestmz_matrix)[3] = "Most abundant m/z"
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
533 spectrum_list[[list_count]] = highestmz_matrix
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
534
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
535
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
536 ## tabular output of spectra values
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
537
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
538 #if $pixel_output:
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
539 print("pixel list")
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
540 pixel_df = Reduce(function(...) merge(..., by=c("x", "y"), all=TRUE), spectrum_list)
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
541 write.table(pixel_df, file="$pixel_tabular_output", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
542 #end if
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
543
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
544 ########################## 8) optional pca image for two components #################
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
545
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
546 #if $do_pca:
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
547
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
548 pca = PCA(msidata, ncomp=2)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
549 par(mfrow = c(2,1))
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
550 plot(pca, col=c("black", "darkgrey"), main="PCA for two components")
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
551 image(pca, col=c("black", "white"), strip=FALSE, ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy))
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
552
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
553 #end if
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
554
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
555 ################## III) properties over spectra index ######################
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
556 ############################################################################
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
557 print("properties over pixels")
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
558 par(mfrow = c(2,1), mar=c(5,6,4,2))
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
559
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
560 ########################## 9) number of peaks per spectrum #################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
561 ## 9a) scatterplot
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
562
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
563 ## order pixels according to annotation groups if annotations are provided
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
564 if (!is.null(levels(msidata\$annotation))){
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
565
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
566 pixel_peaks_df = cbind(pixel_name_df, peaksperpixel)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
567 pixel_ordered = pixel_peaks_df[order(pixel_peaks_df\$pixel_name),] ## order pixels according to annotation group names
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
568 pixel_ordered\$annotation_order = 1:ncol(msidata)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
569 plot_colorByDensity(pixel_ordered\$annotation_order, pixel_ordered\$peaksperpixel, ylab = "", xlab = "", main="Number of peaks per spectrum")
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
570 title(xlab="Spectra index ordered for annotation groups", line=3)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
571 title(ylab="Number of peaks", line=4)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
572 abline(v=abline_vector, lty = 3)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
573 }else{
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
574 plot_colorByDensity(pixels(msidata), peaksperpixel, ylab = "", xlab = "", main="Number of peaks per spectrum")
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
575 title(xlab="Spectra index", line=3)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
576 title(ylab="Number of peaks", line=4)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
577 }
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
578
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
579 ## 9b) histogram
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
580
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
581 hist(peaksperpixel, main="", las=1, xlab = "Number of peaks per spectrum", ylab="")
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
582 title(main="Number of peaks per spectrum", line=2)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
583 title(ylab="Frequency = # spectra", line=4)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
584 abline(v=median(peaksperpixel), col="blue")
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
585
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
586 ## 9c) additional histogram to show contribution of annotation groups
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
587 ## only when pixel annotations were loaded
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
588 if (!is.null(levels(msidata\$annotation))){
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
589
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
590 df_9 = data.frame(peaksperpixel, msidata\$annotation)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
591 colnames(df_9) = c("Npeaks", "annotation")
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
592
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
593 hist_9 = ggplot(df_9, aes(x=Npeaks, fill=annotation)) +
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
594 geom_histogram()+ theme_bw()+
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
595 theme(text=element_text(family="ArialMT", face="bold", size=12))+
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
596 theme(plot.title = element_text(hjust = 0.5))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
597 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
598 theme(legend.position="bottom",legend.direction="vertical")+
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
599 labs(title="Number of peaks per spectrum and annotation group", x="Number of peaks per spectrum", y = "Frequency = # spectra") +
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
600 guides(fill=guide_legend(ncol=5,byrow=TRUE))+
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
601 geom_vline(xintercept = median(peaksperpixel), size = 1, colour = "black",linetype = "dashed")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
602 print(hist_9)}
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
603
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
604 ########################## 10) TIC per spectrum ###########################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
605
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
606 ## 10a)density scatterplot
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
607 par(mfrow = c(2,1), mar=c(5,6,4,2))
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
608
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
609 ## order pixels according to annotation groups if annotations are provided
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
610 if (!is.null(levels(msidata\$annotation))){
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
611
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
612 pixel_TIC_df = cbind(pixel_name_df, TICs)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
613 pixel_ordered = pixel_TIC_df[order(pixel_TIC_df\$pixel_name),] ## order pixels according to annotation group names
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
614 pixel_ordered\$annotation_order = 1:ncol(msidata)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
615
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
616 plot_colorByDensity(pixel_ordered\$annotation_order, pixel_ordered\$TICs, ylab = "", xlab = "", main="TIC per spectrum")
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
617 title(xlab="Spectra index ordered for annotation groups", line=3)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
618 title(ylab="Total ion chromatogram intensity", line=4)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
619 abline(v=abline_vector, lty = 3)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
620 }else{
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
621 plot_colorByDensity(pixels(msidata), TICs, ylab = "", xlab = "", main="TIC per spectrum")
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
622 title(xlab="Spectra index", line=3)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
623 title(ylab = "Total ion chromatogram intensity", line=4)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
624 }
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
625
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
626 ## 10b) histogram
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
627 hist(log(TICs), main="", las=1, xlab = "log(TIC per spectrum)", ylab="")
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
628 title(main= "TIC per spectrum", line=2)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
629 title(ylab="Frequency = # spectra", line=4)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
630 abline(v=median(log(TICs[TICs>0])), col="blue")
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
631
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
632 ## 10c) additional histogram to show annotation contributions
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
633 ## only when pixel annotations were loaded
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
634 if (!is.null(levels(msidata\$annotation))){
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
635 df_10 = data.frame(log(TICs), msidata\$annotation)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
636 colnames(df_10) = c("TICs", "annotation")
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
637
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
638 hist_10 = ggplot(df_10, aes(x=TICs, fill=annotation)) +
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
639 geom_histogram()+ theme_bw()+
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
640 theme(text=element_text(family="ArialMT", face="bold", size=12))+
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
641 theme(plot.title = element_text(hjust = 0.5))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
642 theme(legend.position="bottom",legend.direction="vertical")+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
643 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
644 labs(title="TIC per spectrum and annotation group", x="log(TIC per spectrum)", y = "Frequency = # spectra") +
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
645 guides(fill=guide_legend(ncol=5,byrow=TRUE))+
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
646 geom_vline(xintercept = median(log(TICs[TICs>0])), size = 1, colour = "black",linetype = "dashed")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
647 print(hist_10)}
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
648
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
649 ################################## IV) properties over m/z ####################
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
650 ############################################################################
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
651 print("properties over m/z")
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
652
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
653 ########################## 11) Histogram of m/z values #####################
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
654
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
655 par(mfrow = c(1, 1), cex.axis=1, cex.lab=1, mar=c(5.1,4.1,4.1,2.1))
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
656 hist(mz(msidata), xlab = "m/z", main="Histogram of m/z values")
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
657
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
658 ########################## 12) Number of peaks per m/z #####################
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
659
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
660 peakspermz = rowSums(spectra(msidata)[] > 0 )
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
661
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
662 par(mfrow = c(2,1), mar=c(5,6,4,4.5))
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
663 ## 12a) scatterplot
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
664 plot_colorByDensity(mz(msidata),peakspermz, main= "Number of peaks per m/z", ylab ="")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
665 title(xlab="m/z", line=2.5)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
666 title(ylab = "Number of peaks", line=4)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
667 axis(4, at=pretty(peakspermz),labels=as.character(round((pretty(peakspermz)/pixelcount*100), digits=1)), las=1)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
668 mtext("Coverage of spectra [%]", 4, line=3, adj=1)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
669
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
670 ## 12b) histogram
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
671 hist(peakspermz, main="", las=1, ylab="", xlab="")
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
672 title(ylab = "Frequency", line=4)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
673 title(main="Number of peaks per m/z", xlab = "Number of peaks per m/z", line=2)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
674 abline(v=median(peakspermz), col="blue")
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
675
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
676 ########################## 13) Sum of intensities per m/z ##################
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
677
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
678 ## Sum of all intensities for each m/z (like TIC, but for m/z instead of pixel)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
679 mzTIC = rowSums(spectra(msidata)[]) ## calculate intensity sum for each m/z
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
680
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
681 par(mfrow = c(2,1), mar=c(5,6,4,2))
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
682 ## 13a) scatterplot
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
683 plot_colorByDensity(mz(msidata),mzTIC, main= "Sum of intensities per m/z", ylab ="")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
684 title(xlab="m/z", line=2.5)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
685 title(ylab="Intensity sum", line=4)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
686
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
687 ## 13b) histogram
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
688 hist(log(mzTIC), main="", xlab = "", las=1, ylab="")
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
689 title(main="Sum of intensities per m/z", line=2, ylab="")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
690 title(xlab = "log (sum of intensities per m/z)")
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
691 title(ylab = "Frequency", line=4)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
692 abline(v=median(log(mzTIC[mzTIC>0])), col="blue")
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
693
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
694 ################################## V) intensity plots ########################
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
695 ############################################################################
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
696 print("intensity plots")
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
697 ########################## 14) Intensity distribution ######################
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
698
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
699 par(mfrow = c(2,1), mar=c(5,6,4,2))
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
700
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
701 ## 14a) Median intensity over spectra
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
702 medianint_spectra = apply(spectra(msidata), 2, median)
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
703
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
704 ## order pixels according to annotation groups if annotations are provided
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
705 if (!is.null(levels(msidata\$annotation))){
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
706
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
707 pixel_median_df = cbind(pixel_name_df, medianint_spectra)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
708 pixel_ordered = pixel_median_df[order(pixel_median_df\$pixel_name),] ## order pixels according to annotation group names
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
709 plot(pixel_ordered\$medianint_spectra, main="Median intensity per spectrum",las=1, xlab="Spectra index ordered for annotation groups", ylab="")
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
710 title(ylab="Median spectrum intensity", line=4)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
711 abline(v=abline_vector, lty = 3)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
712 }else{
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
713 plot(medianint_spectra, main="Median intensity per spectrum",las=1, xlab="Spectra index", ylab="")
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
714 title(ylab="Median spectrum intensity", line=4)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
715 }
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
716
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
717 ## 14b) histogram:
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
718 hist(log2(spectra(msidata)[]), main="", xlab = "", ylab="", las=1)
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
719 title(main="Log2-transformed intensities", line=2)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
720 title(xlab="log2 intensities")
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
721 title(ylab="Frequency", line=4)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
722 abline(v=median(log2(spectra(msidata)[(spectra(msidata)>0)])), col="blue")
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
723
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
724 ## 14c) histogram to show contribution of annotation groups
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
725 ## only when annotation tabular was provided
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
726 if (!is.null(levels(msidata\$annotation))){
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
727
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
728 df_13 = data.frame(matrix(,ncol=2, nrow=0))
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
729 for (subsample in levels(msidata\$annotation)){
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
730 log2_int_subsample = log2(spectra(msidata)[,msidata\$annotation==subsample])
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
731 df_subsample = data.frame(as.numeric(log2_int_subsample))
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
732 df_subsample\$annotation = subsample
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
733 df_13 = rbind(df_13, df_subsample)}
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
734 df_13\$annotation = as.factor(df_13\$annotation)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
735 colnames(df_13) = c("logint", "annotation")
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
736
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
737 hist_13 = ggplot(df_13, aes(x=logint, fill=annotation)) +
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
738 geom_histogram()+ theme_bw()+
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
739 theme(text=element_text(family="ArialMT", face="bold", size=12))+
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
740 labs(title="Log2-transformed intensities per sample", x="log2 intensities", y = "Frequency") +
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
741 theme(plot.title = element_text(hjust = 0.5))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
742 theme(legend.position="bottom",legend.direction="vertical")+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
743 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
744 guides(fill=guide_legend(ncol=5,byrow=TRUE))+
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
745 geom_vline(xintercept = median(log2(spectra(msidata)[(spectra(msidata)>0)])), size = 1, colour = "black",linetype = "dashed")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
746 print(hist_13)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
747
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
748 ## 14d) boxplots to visualize in a different way the intensity distributions
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
749 par(mfrow = c(1,1), cex.axis=1.3, cex.lab=1.3, mar=c(13.1,4.1,5.1,2.1))
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
750
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
751 mean_matrix = matrix(,ncol=0, nrow = nrow(msidata))
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
752 for (subsample in levels(msidata\$annotation)){
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
753 mean_mz_sample = rowMeans(spectra(msidata)[,msidata\$annotation==subsample])
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
754 mean_matrix = cbind(mean_matrix, mean_mz_sample)}
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
755
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
756 boxplot(log2(mean_matrix), ylab = "log2 mean intensity per m/z", main="Mean intensities per m/z and annotation group", xaxt = "n")
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
757 (axis(1, at = c(1:number_combined), labels=levels(msidata\$annotation), cex.axis=cex_boxplot, las=2))
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
758 }
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
759
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
760 ################################## VI) Mass spectra and m/z accuracy ########################
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
761 ############################################################################
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
762 print("Mass spectra and m/z accuracy")
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
763
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
764 ############################ 15) Mass spectra ##############################
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
765
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
766 par(mfrow = c(2, 2), cex.axis=1, cex.lab=1, mar=c(5.1,4.1,4.1,2.1))
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
767 pixels_for_plot = c(round(length(pixelnumber)/2, , digits=0), round(length(pixelnumber)/4, , digits=0), round(length(pixelnumber)/4*3, , digits=0))
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
768 plot(msidata, pixel = 1:length(pixelnumber), main= "Average spectrum")
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
769 plot(msidata, pixel = pixels_for_plot[1], main=paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[1],1:2])))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
770 plot(msidata, pixel = pixels_for_plot[2], main= paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[2],1:2])))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
771 plot(msidata, pixel = pixels_for_plot[3], main= paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[3],1:2])))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
772
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
773 ################### 16) Zoomed in mass spectra for calibrants ##############
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
774
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
775 count = 1
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
776 differencevector = numeric()
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
777 differencevector2 = vector()
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
778
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
779 if (length(inputcalibrantmasses) != 0){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
780
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
781 ### calculate plusminus values in m/z for each calibrant, this is used for all following plots
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
782 plusminusvalues = rep($plusminus_ppm/1000000, length(inputcalibrantmasses)) * inputcalibrantmasses
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
783
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
784 for (mass in 1:length(inputcalibrantmasses)){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
785
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
786 ### define the plot window with xmin und xmax
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
787 minmasspixel = features(msidata, mz=inputcalibrantmasses[mass]-1)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
788 maxmasspixel = features(msidata, mz=inputcalibrantmasses[mass]+3)
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
789
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
790 ### find m/z with the highest mean intensity in m/z range (red line in plot 16) and calculate ppm difference for plot 17
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
791 filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],]
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
792
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
793 if (nrow(filtered_data) > 0 & sum(spectra(filtered_data)) > 0){
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
794 maxmassrow = rowMeans(spectra(filtered_data)) ## for each m/z average intensity is calculated
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
795 maxvalue = mz(filtered_data)[which.max(maxmassrow)] ### m/z with highest average intensity in m/z range
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
796 mzdifference = maxvalue - inputcalibrantmasses[mass] ### difference: theoretical value - closest m/z value
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
797 ppmdifference = mzdifference/inputcalibrantmasses[mass]*1000000 ### calculate ppm for accuracy measurement
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
798 }else{
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
799 ppmdifference = NA
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
800 maxvalue = NA}
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
801 differencevector[mass] = round(ppmdifference, digits=2)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
802
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
803 ### find m/z closest to inputcalibrant and calculate ppm difference for plot 18
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
804 mznumber = features(msidata, mz = inputcalibrantmasses[mass]) ### gives featurenumber which is closest to given m/z
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
805 mzvalue = mz(msidata)[mznumber] ### gives closest m/z
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
806 mzdifference2 = mzvalue - inputcalibrantmasses[mass]
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
807 ppmdifference2 = mzdifference2/inputcalibrantmasses[mass]*1000000
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
808 differencevector2[mass] = round(ppmdifference2, digits=2)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
809
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
810 par(mfrow = c(2, 2), oma=c(0,0,2,0))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
811 plot(msidata[minmasspixel:maxmasspixel,], pixel = 1:length(pixelnumber), main= "average spectrum")
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
812 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
813 abline(v=c(maxvalue), col="red", lty=2)
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
814 abline(v=c(mzvalue), col="green2", lty=4)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
815 plot(msidata[minmasspixel:maxmasspixel,], pixel = pixels_for_plot[1], main=paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[1],1:2])))
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
816 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
817 abline(v=c(maxvalue), col="red", lty=2)
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
818 abline(v=c(mzvalue), col="green2", lty=4)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
819 plot(msidata[minmasspixel:maxmasspixel,], pixel = pixels_for_plot[2], main= paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[2],1:2])))
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
820 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
821 abline(v=c(maxvalue), col="red", lty=2)
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
822 abline(v=c(mzvalue), col="green2", lty=4)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
823 plot(msidata[minmasspixel:maxmasspixel,], pixel = pixels_for_plot[3], main= paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[3],1:2])))
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
824 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
825 abline(v=c(maxvalue), col="red", lty=2)
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
826 abline(v=c(mzvalue), col="green2", lty=4)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
827 title(paste0("theor. m/z: ", inputcalibrants[count,1]), col.main="blue", outer=TRUE, line=0, adj=0.074)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
828 title(paste0("most abundant m/z: ", round(maxvalue, digits=4)), col.main="red", outer=TRUE, line=0, adj=0.49)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
829 title(paste0("closest m/z: ", round(mzvalue, digits=4)), col.main="green2", outer=TRUE, line=0, adj=0.93)
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
830
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
831 ### 16b) one large extra plot with different colours for different pixel annotation groups
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
832
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
833 if (!is.null(levels(msidata\$annotation))){
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
834 if (number_combined < 10){
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
835 key_zoomed = TRUE
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
836 }else{key_zoomed = FALSE}
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
837 par(mfrow = c(1, 1))
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
838 plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata),main="Average spectrum per annotation group",
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
839 pixel.groups=msidata\$annotation, key=key_zoomed, col=hue_pal()(number_combined),superpose=TRUE)
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
840 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="black", lty=c(3,1,3))
12
c43a7821c030 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a0cadd9fe40da0094dc87bbf5e06a323973a0b42
galaxyp
parents: 11
diff changeset
841 }
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
842 count=count+1
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
843 }
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
844
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
845 ######### 17) ppm difference input calibrant m/z and m/z with max intensity in given m/z range#########
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
846
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
847 ### plot the ppm difference calculated above: theor. m/z value to highest m/z value:
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
848
7
b86a66dd1a16 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents: 6
diff changeset
849 calibrant_names = as.character(inputcalibrants[,2])
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
850 diff_df = data.frame(differencevector, calibrant_names)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
851
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
852 if (sum(is.na(diff_df[,1])) == nrow(diff_df)){
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
853 plot(0,type='n',axes=FALSE,ann=FALSE)
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
854 title(main=paste("plot 17: no peaks in the chosen region, repeat with higher ppm range")) ## here klammer weggenommen...
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
855 }else{
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
856
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
857 diff_plot1=ggplot(data=diff_df, aes(x=calibrant_names, y=differencevector)) + geom_bar(stat="identity", fill = "darkgray") + theme_minimal() +
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
858 labs(title="Average m/z error (max. average intensity vs. theor. calibrant m/z)", x="calibrants", y = "Average m/z error in ppm")+
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
859 theme(plot.title = element_text(hjust = 0.5, size=14))+theme(text=element_text(family="ArialMT", face="bold", size=16))+
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
860 geom_text(aes(label=differencevector), vjust=-0.3, size=5.5, col="blue") +
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
861 theme(axis.text.x = element_text(angle = 90, hjust = 1, size=16))
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
862
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
863 print(diff_plot1)
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
864 }
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
865
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
866 ######### 18) ppm difference input calibrant m/z and closest m/z ###########
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
867
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
868 ### plot the ppm difference calculated above theor. m/z value to closest m/z value:
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
869
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
870 differencevector2 = round(differencevector2, digits=2)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
871 calibrant_names = as.character(inputcalibrants[,2])
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
872 diff_df = data.frame(differencevector2, calibrant_names)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
873
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
874 diff_plot2=ggplot(data=diff_df, aes(x=calibrant_names, y=differencevector2)) + geom_bar(stat="identity", fill = "darkgray") + theme_minimal() +
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
875 labs(title="Average m/z error (closest measured m/z vs. theor. calibrant m/z)", x="calibrants", y = "Average m/z error in ppm")+
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
876 theme(plot.title = element_text(hjust = 0.5, size=16))+theme(text=element_text(family="ArialMT", face="bold", size=16))+
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
877 geom_text(aes(label=differencevector2), vjust=-0.3, size=5.5, col="blue")+
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
878 theme(axis.text.x = element_text(angle = 90, hjust = 1, size=16))
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
879
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
880 print(diff_plot2)
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
881
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
882 #################### 19) ppm difference over pixels #####################
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
883
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
884 par(mfrow = c(1,1))
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
885 mycolours = c("darkgrey", "darkblue", "blue", "green" , "red", "orange", "yellow", "magenta", "olivedrab1", "lightseagreen")
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
886 count = 1
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
887 ppm_df = as.data.frame(matrix(,ncol=0, nrow = ncol(msidata)))
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
888 for (calibrant in inputcalibrantmasses){
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
889 ### find m/z with the highest mean intensity in m/z range, if no m/z in the range, ppm differences for this calibrant will be NA
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
890 filtered_data = msidata[mz(msidata) >= calibrant-plusminusvalues[count] & mz(msidata) <= calibrant+plusminusvalues[count],]
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
891
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
892 if (nrow(filtered_data) > 0){
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
893 ### filtered for m/z range, find max peak in each spectrum (pixel)(
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
894 ppm_vector = numeric()
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
895 for (pixel_count in 1:ncol(filtered_data)){
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
896 mz_max = mz(filtered_data)[which.max(spectra(filtered_data)[,pixel_count])]
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
897
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
898 mzdiff = mz_max - calibrant
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
899 ppmdiff = mzdiff/calibrant*1000000
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
900
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
901 ### if maximum intensity in m/z range was 0 set ppm diff to NA (not shown in plot)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
902 if (max(spectra(filtered_data)[,pixel_count]) == 0){
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
903 ppmdiff = NA}
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
904 ppm_vector[pixel_count] = ppmdiff}
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
905
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
906 }else{
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
907 ppm_vector = rep(NA, ncol(msidata))
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
908 }
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
909
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
910 ppm_df = cbind(ppm_df, ppm_vector)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
911 count=count+1
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
912 }
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
913
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
914 if (sum(is.na(ppm_df)) == ncol(ppm_df)*nrow(ppm_df)){
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
915 plot(0,type='n',axes=FALSE,ann=FALSE)
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
916 title(main=paste("plot 19: no peaks in the chosen region, repeat with higher ppm range"))
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
917 }else{
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
918
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
919 ### plot ppm differences over pixels (spectra index)
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
920 par(mar=c(4.1, 4.1, 4.1, 7.5))
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
921
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
922 ## if annotations are provided, pixel index is ordered according to annotation groups
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
923 if (!is.null(levels(msidata\$annotation))){
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
924 ppm_df_pixels =cbind(pixel_name_df, ppm_df)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
925 pixel_ordered = ppm_df_pixels[order(ppm_df_pixels\$pixel_name),] ## order pixels according to annotation group names
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
926
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
927 plot(0,0,type="n", ylim=c(min(ppm_df, na.rm=TRUE),max(ppm_df, na.rm=TRUE)), xlim = c(1,ncol(filtered_data)),xlab = "Spectra index ordered for annotation groups", ylab = "m/z difference in ppm", main="Difference m/z with max. average intensity vs. theor. m/z\n(per spectrum)")
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
928
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
929 for (each_cal in 1:ncol(ppm_df)){
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
930 lines(pixel_ordered[,each_cal+2], col=mycolours[each_cal], type="p")}
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
931 legend("topright", inset=c(-0.25,0), xpd = TRUE, bty="n", legend=inputcalibrantmasses, col=mycolours[1:ncol(ppm_df)],lty=1)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
932 abline(v=abline_vector, lty = 3)
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
933 }else{
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
934
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
935 plot(0,0,type="n", ylim=c(min(ppm_df, na.rm=TRUE),max(ppm_df, na.rm=TRUE)), xlim = c(1,ncol(filtered_data)),xlab = "Spectra index", ylab = "m/z difference in ppm", main="Difference m/z with max. average intensity vs. theor. m/z\n(per spectrum)")
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
936
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
937 for (each_cal in 1:ncol(ppm_df)){
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
938 lines(ppm_df[,each_cal], col=mycolours[each_cal], type="p")}
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
939 legend("topright", inset=c(-0.25,0), xpd = TRUE, bty="n", legend=inputcalibrantmasses, col=mycolours[1:ncol(ppm_df)],lty=1)}
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
940 }
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
941
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
942 }else{print("plot 16+17+18+19) The inputcalibrant m/z were not provided or outside the m/z range")}
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
943 }else{
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
944 print("inputfile has no intensities > 0")
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
945 }
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
946 dev.off()
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
947
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
948
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
949 ]]></configfile>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
950 </configfiles>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
951 <inputs>
3
f6aa0cff777c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
diff changeset
952 <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
953 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
954 <conditional name="processed_cond">
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
955 <param name="processed_file" type="select" label="Is the input file a processed imzML file ">
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
956 <option value="no_processed" selected="True">not a processed imzML</option>
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
957 <option value="processed">processed imzML</option>
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
958 </param>
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
959 <when value="no_processed"/>
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
960 <when value="processed">
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
961 <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
962 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
963 <option value="mz" >mz</option>
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
964 <option value="ppm" selected="True" >ppm</option>
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
965 </param>
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
966 </when>
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
967 </conditional>
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
968 <conditional name="tabular_annotation">
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
969 <param name="load_annotation" type="select" label="Use pixel annotation from tabular file for QC plots">
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
970 <option value="no_annotation" selected="True">pixels belong into one group only</option>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
971 <option value="yes_annotation">use pixel annotation from a tabular file</option>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
972 </param>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
973 <when value="yes_annotation">
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
974 <param name="annotation_file" type="data" format="tabular" label="Use annotations from tabular file"
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
975 help="Tabular file with three columns: x values, y values and pixel annotations"/>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
976 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
977 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
978 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
979 </when>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
980 <when value="no_annotation"/>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
981 </conditional>
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
982 <param name="filename" type="text" value="" optional="true" label="Title" help="will appear as header in the quality report, if nothing given input dataset name is used"/>
4
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
983 <param name="calibrant_file" type="data" optional="true" format="tabular"
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
984 label="File with internal calibrants" help="first column: m/z, second column: name (optional), tabular file"/>
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
985 <param name="plusminus_ppm" value="50" type="float" label="ppm range" help="Will be added in both directions to input calibrant m/z"/>
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
986 <param name="do_pca" type="boolean" display="radio" label="PCA with 2 components"/>
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
987 <repeat name="calibrantratio" title="Plot fold change of two m/z" min="0" max="10">
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
988 <param name="mass1" value="1111" type="float" label="M/z 1" help="First m/z"/>
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
989 <param name="mass2" value="2222" type="float" label="M/z 2" help="Second m/z"/>
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
990 <param name="distance" value="0.25" type="float" label="M/z range" help="Plusminus m/z window added to input m/z. In both m/z ranges the maximum intensity is used to calculate the fold change"/>
3
f6aa0cff777c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
diff changeset
991 <param name="filenameratioplot" type="text" optional="true" label="Title" help="Optional title for fold change plot."/>
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
992 </repeat>
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
993 <param name="pixel_output" type="boolean" display="radio" label="Tabular output with spectra information"/>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
994 </inputs>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
995 <outputs>
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
996 <data format="pdf" name="plots" from_work_dir="qualitycontrol.pdf" label = "$infile.display_name QC_report"/>
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
997 <data format="tabular" name="pixel_tabular_output" label="$infile.display_name spectra information">
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
998 <filter>pixel_output</filter>
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
999 </data>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1000 </outputs>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1001 <tests>
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1002 <test expect_num_outputs="2">
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1003 <param name="infile" value="" ftype="imzml">
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1004 <composite_data value="Example_Processed.imzML"/>
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1005 <composite_data value="Example_Processed.ibd"/>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1006 </param>
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1007 <conditional name="processed_cond">
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1008 <param name="processed_file" value="processed"/>
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1009 <param name="accuracy" value="200"/>
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1010 <param name="units" value="ppm"/>
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1011 </conditional>
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1012 <conditional name="tabular_annotation">
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1013 <param name="load_annotation" value="no_annotation"/>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1014 </conditional>
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1015 <param name="calibrant_file" value="inputcalibrantfile1.txt"/>
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1016 <param name="plusminus_ppm" value="100"/>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1017 <param name="filename" value="Testfile_imzml"/>
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
1018 <param name="do_pca" value="True"/>
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
1019 <repeat name="calibrantratio">
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1020 <param name="mass1" value="328.9"/>
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1021 <param name="mass2" value="398.8"/>
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
1022 <param name="distance" value="0.25"/>
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1023 <param name="filenameratioplot" value = "Ratio of mass1 (328.9) / mass2 (398.8)"/>
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
1024 </repeat>
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1025 <param name="pixel_output" value="True"/>
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1026 <output name="pixel_tabular_output" file="spectra_info_imzml.txt"/>
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1027 <output name="plots" file="QC_imzml.pdf" compare="sim_size" delta="20000"/>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1028 </test>
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1029
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1030 <test expect_num_outputs="1">
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1031 <param name="infile" value="" ftype="analyze75">
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
1032 <composite_data value="Analyze75.hdr"/>
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
1033 <composite_data value="Analyze75.img"/>
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
1034 <composite_data value="Analyze75.t2m"/>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1035 </param>
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1036 <conditional name="tabular_annotation">
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1037 <param name="load_annotation" value="no_annotation"/>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1038 </conditional>
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1039 <param name="calibrant_file" value="inputcalibrantfile2.txt"/>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1040 <param name="filename" value="Testfile_analyze75"/>
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
1041 <param name="do_pca" value="True"/>
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1042 <output name="plots" file="QC_analyze75.pdf" compare="sim_size" delta="20000"/>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1043 </test>
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1044
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1045 <test expect_num_outputs="2">
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1046 <param name="infile" value="123_combined.RData" ftype="rdata"/>
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1047
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1048 <conditional name="tabular_annotation">
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1049 <param name="load_annotation" value="yes_annotation"/>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1050 <param name="annotation_file" value="annotations_rdata.tabular"/>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1051 <param name="column_x" value="1"/>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1052 <param name="column_y" value="2"/>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1053 <param name="column_names" value="3"/>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1054 </conditional>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1055 <param name="calibrant_file" value="inputcalibrantfile1.txt"/>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1056 <param name="plusminus_ppm" value="100"/>
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1057 <param name="filename" value="Testfile_rdata"/>
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
1058 <param name="do_pca" value="True"/>
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1059 <param name="pixel_output" value="True"/>
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1060 <output name="pixel_tabular_output" file="spectra_info_123_combi.txt"/>
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1061 <output name="plots" file="QC_rdata.pdf" compare="sim_size" delta="20000"/>
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1062 </test>
10
3eee933c27cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1063 <test expect_num_outputs="1">
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1064 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/>
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1065 <conditional name="tabular_annotation">
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1066 <param name="load_annotation" value="no_annotation"/>
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1067 </conditional>
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1068 <param name="calibrant_file" value="inputcalibrantfile2.txt"/>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1069 <param name="filename" value="Testfile_rdata"/>
13
88e12d270e35 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
1070 <param name="do_pca" value="False"/>
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1071 <output name="plots" file="QC_empty_spectra.pdf" compare="sim_size" delta="20000"/>
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
1072 </test>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1073 </tests>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1074 <help>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1075 <![CDATA[
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1076 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1077
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1078 This tool uses Cardinal to read files and create a quality control report with descriptive plots for mass spectrometry imaging data.
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1079
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1080 Input data: 3 types of input data can be used:
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1081
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1082 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1083 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1084 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1085 - optional: tabular file with pixel annotations: x and y values in separate columns and the corresponding annotation in a third column
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1086
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1087 Options:
4
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
1088
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1089 - internal calibrants are used for m/z heatmaps (x-y grid), heatmap of number of calibrants per spectrum (x-y grid), zoomed in mass spectra, m/z accuracy
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1090 - optional fold change plot: draws a heatmap (x-y grid) for the fold change of two m/z (log2(intensity ratio))
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1091
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1092 Output:
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1093
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1094 - quality control report as pdf with key numbers and descriptive plots describing the mass spectrometry imaging data
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1095 - optional spectra information as tabular file with annotation (if provided), numbers of calibrants (needs valid calibrants), numbers of peaks, TIC and most abundant m/z in each spectrum
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1096
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1097 Tip:
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1098
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1099 - For additional m/z heatmaps use the MSI ion images tool and to plot more mass spectra use the MSI mass spectra tool.
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1100
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1101 ----------------------------------------------------------------------------------------------------------------------------------------------------
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1102
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1103 Overview of the QC report plots:
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1104
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1105 - (annot): this plots will only be drawn if pixel annotations are loaded via a tabular file
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1106 - (cal): this plots will only be drawn if a tabular file with at least one valid calibrant m/z is provided
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1107 - (FC): this plots will only be drawn if the optional fold change image is selected
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1108 - Vertical lines in histograms represent median values. In density scatter plots the colour changes from blue to green, yellow and red the more points are overlayed.
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1109
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1110 - Overview of file properties: Numbers and ranges for m/z features and pixels are given. Median and range across all intensity values are provided. Intensities > 0 gives the percentage of m/z-pixel pairs with an intensity above zero. The number of empty spectra (TIC = 0), the median number of peaks (intensities > 0) per spectra as well as the median TIC (total ion chromatogram) are given. The processing status of the file is provided as well as the number of valid calibrants from the provided tabular file.> 0 (Intensities > 0).
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1111
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1112 x-y images (pixel/spectra information):
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1113
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1114 - (annot) Spatial orientation of annotated pixel: All pixels of one annotation group have the same colour.
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1115 - Pixel order: Shows the order of the pixels in the provided file. Depending on the instrument this can represent the acquisition order. If annotation file is provided pixels are ordered according to annotation groups.
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1116 - (cal) Number of calibrants per pixel: In every spectrum the calibrant m/z window (calibrant m/z plusminus 'ppm range') is searched for peaks (intensity > 0). Calibrants are considered present in a spectrum when they have at least one peak in their m/z window.
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1117 - (FC) Control of fold change plot: For both input m/z a zoomed in average spectrum is drawn with the input m/z as blue dashed line, the m/z range as blue dotted lines and the maximum intensity in the m/z window with a red line.
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1118 - (FC) Fold change image: For each spectrum the intensities of the two optimal m/z features (red lines in control plots) are divided and log2 transformed to obtain the fold change, which is then plotted as a heatmap.
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1119 - (cal) Intensity heatmaps for the m/z value that is closest to the calibrant m/z. The intensities are averaged within the calibrant m/z window (ppm range).
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1120 - Number of peaks per spectrum: For each spectrum the number of m/z values with intensity > 0 is calculated and plotted as heatmap.
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1121 - Total ion chromatogram: For each spectrum all intensities are summed up to obtain the TIC which is plotted as heatmap.
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1122 - Most abundant m/z in each spectrum: For each spectrum the m/z value with the highest intensity is plotted.
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1123 - PCA for two components: Result of a principal component analysis (PCA) for two components is given. The loading plot depicts the contribution of each m/z value and the x-y image represents the differences between the pixels.
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1124
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1125 Properties over spectra/pixels:
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1126
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1127 - Number of peaks per spectrum: Scatter plot and histogram showing the number of intensities > 0 for each spectrum. If annotation tabular file is provided, the pixels are sorted according to annotation groups and the dotted lines in the scatter plot separate spectra of different annotation groups.
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1128 - (annot) Number of peaks per spectrum and annotation group: Same histogram as in plot before but with colours to show the contribution of each pixel annotation group.
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1129 - TIC per spectrum: Scatter plot and histogram showing the sum of all intensities per spectrum (TIC). Dotted lines in the scatter plot separate spectra of different annotation groups.
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1130 - (annot) TIC per spectrum and annotation group: Same histogram as in plot before but with colours to show the contribution of each pixel annotation group.
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1131
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1132 Properties over m/z features:
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1133
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1134 - Histogram of m/z values: Histogram of all m/z values (complete m/z axis)
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1135 - Number of peaks per m/z: Scatter plot and histogram giving the number of intensities > 0 for each m/z.
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1136 - Sum of intensities per m/z: Scatter plot and histogram of the sum of all intensities per m/z.
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1137
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1138 Intensity plots:
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1139
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1140 - Median intensity per spectrum: Scatter plot in which each point represents the median intensity for one spectrum. Dotted lines in the scatter plot separate spectra of different annotation groups.
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1141 - Log2-transformed intensities: Histogram of log2-transformed intensities.
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1142 - (annot) log2-transformed intensities per annotation group: Same histogram as before but with colours to show the contribution of each pixel annotation group.
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1143 - (annot) Mean intensities per m/z and annotation group: For all pixels of an annotation group the mean intensity for each m/z is calculated and shown as boxplot.
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1144
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1145 Mass spectra and m/z accuracy:
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1146
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1147 - Mass spectra over the full m/z range: First plot shows the average intensities over all spectra. The other three mass spectra are from single pixels (spectra).
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1148 - (cal) For each calibrant four zoomed in mass spectrum are drawn: The first shows the average intensities over all spectra and the other three are single mass spectra. The theoretical calibrant m/z (taken from the input file) is represented by the dashed blue line. The dotted blue lines show the given ppm range. The green line is the m/z value that is closest to the theoretical calibrant and the red line is the m/z with the highest average intensity in the m/z window.
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1149 - (annot) Average spectrum per annotation group: For each calibrant a zoomed in mass spectrum is plotted this time with the average intensities for each annotation group separately.
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1150 - (cal) Difference m/z with max. average intensity vs. theor. calibrant m/z: The difference in ppm between the m/z with the highest average intensity and the theoretical m/z are plotted for each calibrant. This corresponds to the difference between the dashed blue line and the red line in the zoomed in mass spectra.
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1151 - (cal) Difference closest measured m/z vs. theor. calibrant m/z: The difference in ppm between the closest m/z value and the theoretical m/z values are plotted for each calibrant. This corresponds to the difference between the dashed blue line and the green line in the zoomed in mass spectra.
14
7c7c39b9ec4a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1152 - (cal) Difference m/z with max. average intensity vs. theor. m/z (per spectrum): For each spectrum the ppm difference between the m/z with the highest average intensity and the theoretical m/z are plotted. The calibrants have different plotting colours. Dashed lines separate spectra of different annotation groups.
11
30d0aabb1b46 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1153
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1154
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1155 ]]>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1156 </help>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1157 <citations>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1158 <citation type="doi">10.1093/bioinformatics/btv146</citation>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1159 </citations>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1160 </tool>
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
1161