cardinal_classification: classification.xml annotate

annotate classification.xml @ 14:ece627528a78 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"

author	galaxyp
date	Fri, 07 May 2021 10:10:35 +0000
parents	24c000517173
children	f28ad96b76dc

rev	line source
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	1 <tool id="cardinal_classification" name="MSI classification" version="@VERSION@.1">
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	2 <description>spatial classification of mass spectrometry imaging data</description>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	3 <macros>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	4 <import>macros.xml</import>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	5 </macros>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	6 <expand macro="requirements">
1 6a03b201bc12 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c galaxyp parents: 0 diff changeset	7 <requirement type="package" version="2.3">r-gridextra</requirement>
9 24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	8 <requirement type="package" version="3.3.2">r-ggplot2</requirement>
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	9 </expand>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	10 <command detect_errors="exit_code">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	11 <![CDATA[
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	12
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	13 @INPUT_LINKING@
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	14 cat '${MSI_segmentation}' &&
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	15 Rscript '${MSI_segmentation}'
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	16
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	17 ]]>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	18 </command>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	19 <configfiles>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	20 <configfile name="MSI_segmentation"><![CDATA[
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	21
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	22
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	23 ################################# load libraries and read file #########################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	24
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	25 library(Cardinal)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	26 library(gridExtra)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	27 library(ggplot2)
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	28 library(scales)
7 6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 4 diff changeset	29
6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 4 diff changeset	30 @READING_MSIDATA@
6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 4 diff changeset	31
6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 4 diff changeset	32 msidata = as(msidata, "MSImageSet") ##coercion to MSImageSet
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	33
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	34
3 585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	35 ## remove duplicated coordinates
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	36 msidata <- msidata[,!duplicated(coord(msidata))]
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	37
2 cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	38 @DATA_PROPERTIES_INRAM@
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	39
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	40
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	41 ######################################## PDF ###################################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	42 ################################################################################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	43 ################################################################################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	44
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	45 Title = "Prediction"
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	46
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	47 #if str( $type_cond.type_method) == "training":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	48
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	49 Title = "$type_cond.method_cond.class_method"
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	50 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	51
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	52 pdf("classificationpdf.pdf", fonts = "Times", pointsize = 12)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	53 plot(0,type='n',axes=FALSE,ann=FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	54
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	55
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	56 title(main=paste0(Title," for file: \n\n", "$infile.display_name"))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	57
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	58
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	59 ##################### I) numbers and control plots #############################
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	60 ################################################################################
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	61
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	62 ## table with values
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	63 grid.table(property_df, rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	64
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	65
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	66 if (npeaks > 0 && sum(is.na(spectra(msidata)))==0){
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	67
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	68 opar <- par()
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	69
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	70 ######################## II) Training #######################################
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	71 #############################################################################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	72 #if str( $type_cond.type_method) == "training":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	73 print("training")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	74
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	75
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	76 ## load y response (will be needed in every training scenario)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	77
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	78 y_tabular = read.delim("$type_cond.annotation_file", header = $type_cond.tabular_header, stringsAsFactors = FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	79
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	80 #if str($type_cond.column_fold) == "None":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	81 y_input = y_tabular[,c($type_cond.column_x, $type_cond.column_y, $type_cond.column_response)]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	82 #else
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	83 y_input = y_tabular[,c($type_cond.column_x, $type_cond.column_y, $type_cond.column_response, $type_cond.column_fold)]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	84 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	85
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	86 colnames(y_input)[1:2] = c("x", "y")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	87 ## merge with coordinate information of msidata
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	88 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	89 colnames(msidata_coordinates)[3] = "pixel_index"
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	90 merged_response = merge(msidata_coordinates, y_input, by=c("x", "y"), all.x=TRUE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	91 merged_response[is.na(merged_response)] = "NA"
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	92 merged_response = merged_response[order(merged_response\$pixel_index),]
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	93 conditions = as.factor(merged_response[,4])
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	94 y_vector = conditions
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	95
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	96 ## plot of y vector
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	97
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	98 position_df = cbind(coord(msidata)[,1:2], conditions)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	99 y_plot = ggplot(position_df, aes(x=x, y=y, fill=conditions))+
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	100 geom_tile() +
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	101 coord_fixed()+
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	102 ggtitle("Distribution of the conditions")+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	103 theme_bw()+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	104 theme(
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	105 plot.background = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	106 panel.grid.major = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	107 panel.grid.minor = element_blank())+
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	108 theme(text=element_text(family="ArialMT", face="bold", size=15))+
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	109 theme(legend.position="bottom",legend.direction="vertical")+
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	110 guides(fill=guide_legend(ncol=4,byrow=TRUE))
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	111 coord_labels = aggregate(cbind(x,y)~conditions, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	112 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$conditions)
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	113 print(y_plot)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	114
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	115
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	116 ## plot of folds
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	117
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	118 #if str($type_cond.column_fold) != "None":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	119 fold_vector = as.factor(merged_response[,5])
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	120
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	121
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	122 position_df = cbind(coord(msidata)[,1:2], fold_vector)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	123 fold_plot = ggplot(position_df, aes(x=x, y=y, fill=fold_vector))+
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	124 geom_tile() +
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	125 coord_fixed()+
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	126 ggtitle("Distribution of the fold variable")+
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	127 theme_bw()+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	128 theme(
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	129 plot.background = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	130 panel.grid.major = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	131 panel.grid.minor = element_blank())+
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	132 theme(text=element_text(family="ArialMT", face="bold", size=15))+
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	133 theme(legend.position="bottom",legend.direction="vertical")+
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	134 guides(fill=guide_legend(ncol=4,byrow=TRUE))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	135 coord_labels = aggregate(cbind(x,y)~fold_vector, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	136 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$fold_vector)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	137 print(fold_plot)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	138
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	139 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	140
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	141 ######################## PLS #############################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	142 #if str( $type_cond.method_cond.class_method) == "PLS":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	143 print("PLS")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	144
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	145 ######################## PLS - CV #############################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	146 #if str( $type_cond.method_cond.analysis_cond.PLS_method) == "cvapply":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	147 print("PLS cv")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	148
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	149 ## set variables for components and number of response groups
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	150 components = c($type_cond.method_cond.analysis_cond.plscv_comp)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	151 number_groups = length(levels(y_vector))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	152
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	153 ## PLS-cvApply:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	154 msidata.cv.pls <- cvApply(msidata, .y = y_vector, .fold = fold_vector, .fun = "PLS", ncomp = components)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	155
2 cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	156 ## remove msidata to clean up RAM space
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	157 rm(msidata)
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	158 gc()
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	159
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	160 ## create table with summary
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	161 count = 1
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	162 summary_plscv = list()
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	163 accuracy_vector = numeric()
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	164 for (iteration in components){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	165 summary_iteration = summary(msidata.cv.pls)\$accuracy[[paste0("ncomp = ", iteration)]]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	166 ## change class of numbers into numeric to round and calculate mean
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	167 summary_iteration2 = round(as.numeric(summary_iteration), digits=2)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	168 summary_matrix = matrix(summary_iteration2, nrow=4, ncol=number_groups)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	169 accuracy_vector[count] = mean(summary_matrix[1,]) ## vector with accuracies to find later maximum for plot
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	170 summary_iteration3 = cbind(rownames(summary_iteration), summary_matrix) ## include rownames in table
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	171 summary_iteration4 = t(summary_iteration3)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	172 summary_iteration5 = cbind(c(paste0("ncomp = ", iteration), colnames(summary_iteration)), summary_iteration4)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	173 summary_plscv[[count]] = summary_iteration5
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	174 count = count+1} ## create list with summary table for each component
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	175 summary_plscv = do.call(rbind, summary_plscv)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	176 summary_df = as.data.frame(summary_plscv)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	177 colnames(summary_df) = NULL
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	178
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	179 ## plots
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	180 ## plot to find ncomp with highest accuracy
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	181 plot(components, accuracy_vector, ylab = "mean accuracy",type="o", main="Mean accuracy of PLS classification")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	182 ncomp_max = components[which.max(accuracy_vector)] ## find ncomp with max. accuracy
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	183 ## one image for each sample/fold, 4 images per page
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	184 minimumy = min(coord(msidata.cv.pls)[,2])
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	185 maximumy = max(coord(msidata.cv.pls)[,2])
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	186 image(msidata.cv.pls, model = list(ncomp = ncomp_max),ylim= c(maximumy+0.2maximumy,minimumy-0.2minimumy),layout = c(1, 1))
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	187
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	188 ## print table with summary in pdf
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	189 par(opar)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	190 plot(0,type='n',axes=FALSE,ann=FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	191 title(main="Summary for the different components\n", adj=0.5)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	192 ## 20 rows fits in one page:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	193 if (nrow(summary_df)<=20){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	194 grid.table(summary_df, rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	195 }else{
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	196 grid.table(summary_df[1:20,], rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	197 mincount = 21
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	198 maxcount = 40
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	199 for (count20 in 1:(ceiling(nrow(summary_df)/20)-1)){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	200 plot(0,type='n',axes=FALSE,ann=FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	201 if (maxcount <= nrow(summary_df)){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	202 grid.table(summary_df[mincount:maxcount,], rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	203 mincount = mincount+20
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	204 maxcount = maxcount+20
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	205 }else{### stop last page with last sample otherwise NA in table
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	206 grid.table(summary_df[mincount:nrow(summary_df),], rows= NULL)}
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	207 }
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	208 }
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	209
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	210 ## optional output as .RData
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	211 #if $output_rdata:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	212 save(msidata.cv.pls, file="$classification_rdata")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	213 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	214
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	215
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	216 ######################## PLS - analysis ###########################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	217 #elif str( $type_cond.method_cond.analysis_cond.PLS_method) == "PLS_analysis":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	218 print("PLS analysis")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	219
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	220 ## set variables for components and number of response groups
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	221 component = c($type_cond.method_cond.analysis_cond.pls_comp)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	222 number_groups = length(levels(y_vector))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	223
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	224 ### stop if multiple values for PLS components are selected what sets component to 0
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	225 tryCatch(
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	226 {
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	227
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	228 if (component==0)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	229 {
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	230 stop(call.=FALSE)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	231 }
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	232 },
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	233 error=function(cond) {
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	234 ## in case user used multiple inputs for component - this is only possible in cv apply
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	235 message("Error during PLS training")
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	236 message("Possible problems: Multiple values for component were selected - this is only possible in cvapply but not for PLS analysis or component was set to 0 but minimum for component is 1)")
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	237 stop(call.=FALSE)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	238 }
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	239 )
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	240
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	241 ### pls analysis and coefficients plot
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	242 msidata.pls <- PLS(msidata, y = y_vector, ncomp = component, scale=$type_cond.method_cond.analysis_cond.pls_scale)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	243 plot(msidata.pls, main="PLS coefficients per m/z")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	244
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	245 ### summary table of PLS
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	246 summary_table = summary(msidata.pls)\$accuracy[[paste0("ncomp = ",component)]]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	247 summary_table2 = round(as.numeric(summary_table), digits=2)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	248 summary_matrix = matrix(summary_table2, nrow=4, ncol=number_groups)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	249 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	250 summary_table4 = t(summary_table3)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	251 summary_table5 = cbind(c(paste0("ncomp = ", component), colnames(summary_table)), summary_table4)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	252 plot(0,type='n',axes=FALSE,ann=FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	253 grid.table(summary_table5, rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	254
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	255 ### image of the best m/z
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	256 minimumy = min(coord(msidata)[,2])
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	257 maximumy = max(coord(msidata)[,2])
7 6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 4 diff changeset	258 print(image(msidata, mz = topFeatures(msidata.pls)[1,1], normalize.image = "linear", contrast.enhance = "histogram",ylim= c(maximumy+0.2maximumy,minimumy-0.2minimumy), smooth.image="gaussian", main="best m/z heatmap"))
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	259
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	260 ### m/z and pixel information output
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	261 pls_classes = data.frame(msidata.pls\$classes[[1]])
3 585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	262 ## pixel names and coordinates
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	263 ## to remove potential sample names and z dimension, split at comma and take only x and y
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	264 x_coords = unlist(lapply(strsplit(names(pixels(msidata)), ","), `[[`, 1))
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	265 y_coords = unlist(lapply(strsplit(names(pixels(msidata)), ","), `[[`, 2))
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	266 x_coordinates = gsub("x = ","",x_coords)
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	267 y_coordinates = gsub(" y = ","",y_coords)
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	268 pixel_names = paste0("xy_", x_coordinates, "_", y_coordinates)
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	269
2 cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	270 ## remove msidata to clean up RAM space
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	271 rm(msidata)
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	272 gc()
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	273 pls_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, pls_classes)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	274 colnames(pls_classes2) = c("pixel names", "x", "y","predicted condition")
7 6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 4 diff changeset	275 pls_toplabels = topFeatures(msidata.pls, n=Inf)
2 cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	276 pls_toplabels[,4:6] <-round(pls_toplabels[,4:6],6)
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	277 write.table(pls_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	278 write.table(pls_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	279
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	280 ## image with predicted classes
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	281 prediction_df = cbind(coord(msidata.pls)[,1:2], pls_classes)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	282 colnames(prediction_df) = c("x", "y", "predicted_classes")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	283
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	284 prediction_plot = ggplot(prediction_df, aes(x=x, y=y, fill=predicted_classes))+
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	285 geom_tile() +
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	286 coord_fixed()+
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	287 ggtitle("Predicted condition for each pixel")+
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	288 theme_bw()+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	289 theme(
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	290 plot.background = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	291 panel.grid.major = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	292 panel.grid.minor = element_blank())+
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	293 theme(text=element_text(family="ArialMT", face="bold", size=15))+
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	294 theme(legend.position="bottom",legend.direction="vertical")+
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	295 guides(fill=guide_legend(ncol=4,byrow=TRUE))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	296 coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	297 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	298 print(prediction_plot)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	299
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	300 ### optional output as .RData
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	301 #if $output_rdata:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	302 save(msidata.pls, file="$classification_rdata")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	303 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	304
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	305 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	306
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	307 ######################## OPLS #############################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	308 #elif str( $type_cond.method_cond.class_method) == "OPLS":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	309 print("OPLS")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	310
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	311 ######################## OPLS -CV #############################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	312 #if str( $type_cond.method_cond.opls_analysis_cond.opls_method) == "opls_cvapply":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	313 print("OPLS cv")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	314
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	315 ## set variables for components and number of response groups
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	316 components = c($type_cond.method_cond.opls_analysis_cond.opls_cvcomp)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	317 number_groups = length(levels(y_vector))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	318
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	319 ## OPLS-cvApply:
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	320 msidata.cv.opls <- cvApply(msidata, .y = y_vector, .fold = fold_vector, .fun = "OPLS", ncomp = components)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	321 ## for use to reduce msidata: keep.Xnew = $type_cond.method_cond.opls_analysis_cond.xnew_cv
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	322
2 cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	323 ## remove msidata to clean up RAM space
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	324 rm(msidata)
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	325 gc()
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	326
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	327 ## create table with summary
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	328 count = 1
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	329 summary_oplscv = list()
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	330 accuracy_vector = numeric()
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	331 for (iteration in components){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	332
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	333 summary_iteration = summary(msidata.cv.opls)\$accuracy[[paste0("ncomp = ", iteration)]]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	334 ## change class of numbers into numeric to round and calculate mean
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	335 summary_iteration2 = round(as.numeric(summary_iteration), digits=2)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	336 summary_matrix = matrix(summary_iteration2, nrow=4, ncol=number_groups)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	337 accuracy_vector[count] = mean(summary_matrix[1,]) ## vector with accuracies to find later maximum for plot
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	338 summary_iteration3 = cbind(rownames(summary_iteration), summary_matrix) ## include rownames in table
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	339 summary_iteration4 = t(summary_iteration3)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	340 summary_iteration5 = cbind(c(paste0("ncomp = ", iteration), colnames(summary_iteration)), summary_iteration4)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	341 summary_oplscv[[count]] = summary_iteration5
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	342 count = count+1} ## create list with summary table for each component
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	343 summary_oplscv = do.call(rbind, summary_oplscv)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	344 summary_df = as.data.frame(summary_oplscv)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	345 colnames(summary_df) = NULL
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	346
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	347 ## plots
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	348 ## plot to find ncomp with highest accuracy
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	349 plot(components, accuracy_vector, ylab = "mean accuracy", type="o", main="Mean accuracy of OPLS classification")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	350 ncomp_max = components[which.max(accuracy_vector)] ## find ncomp with max. accuracy
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	351 ## one image for each sample/fold, 4 images per page
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	352 minimumy = min(coord(msidata.cv.opls)[,2])
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	353 maximumy = max(coord(msidata.cv.opls)[,2])
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	354 image(msidata.cv.opls, model = list(ncomp = ncomp_max),ylim= c(maximumy+0.2maximumy,minimumy-0.2minimumy),layout = c(1, 1))
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	355
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	356 ## print table with summary in pdf
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	357 par(opar)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	358 plot(0,type='n',axes=FALSE,ann=FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	359 title(main="Summary for the different components\n", adj=0.5)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	360 ## 20 rows fits in one page:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	361 if (nrow(summary_df)<=20){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	362 grid.table(summary_df, rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	363 }else{
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	364 grid.table(summary_df[1:20,], rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	365 mincount = 21
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	366 maxcount = 40
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	367 for (count20 in 1:(ceiling(nrow(summary_df)/20)-1)){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	368 plot(0,type='n',axes=FALSE,ann=FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	369 if (maxcount <= nrow(summary_df)){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	370 grid.table(summary_df[mincount:maxcount,], rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	371 mincount = mincount+20
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	372 maxcount = maxcount+20
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	373 }else{### stop last page with last sample otherwise NA in table
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	374 grid.table(summary_df[mincount:nrow(summary_df),], rows= NULL)}
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	375 }
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	376 }
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	377
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	378 ## optional output as .RData
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	379 #if $output_rdata:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	380 save(msidata.cv.opls, file="$classification_rdata")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	381 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	382
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	383
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	384 ######################## OPLS -analysis ###########################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	385 #elif str( $type_cond.method_cond.opls_analysis_cond.opls_method) == "opls_analysis":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	386 print("OPLS analysis")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	387
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	388 ## set variables for components and number of response groups
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	389 component = c($type_cond.method_cond.opls_analysis_cond.opls_comp)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	390 number_groups = length(levels(y_vector))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	391
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	392 ### stop if multiple values for OPLS components are selected what sets component to 0
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	393 tryCatch(
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	394 {
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	395
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	396 if (component==0)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	397 {
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	398 stop(call.=FALSE)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	399 }
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	400 },
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	401 error=function(cond) {
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	402 ## in case user used multiple inputs for component - this is only possible in cv apply
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	403 message("Error during OPLS training")
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	404 message("Possible problems: Multiple values for component were selected - this is only possible in cvapply but not for OPLS analysis or component was set to 0 but minimum for component is 1)")
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	405 stop(call.=FALSE)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	406 }
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	407 )
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	408
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	409 ### opls analysis and coefficients plot
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	410 msidata.opls <- PLS(msidata, y = y_vector, ncomp = component, scale=$type_cond.method_cond.opls_analysis_cond.opls_scale)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	411 ## to reduce msidata: keep.Xnew = $type_cond.method_cond.opls_analysis_cond.xnew
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	412 plot(msidata.opls, main="OPLS coefficients per m/z")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	413
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	414
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	415 ### summary table of OPLS
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	416 summary_table = summary(msidata.opls)\$accuracy[[paste0("ncomp = ",component)]]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	417 summary_table2 = round(as.numeric(summary_table), digits=2)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	418 summary_matrix = matrix(summary_table2, nrow=4, ncol=number_groups)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	419 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	420 summary_table4 = t(summary_table3)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	421 summary_table5 = cbind(c(paste0("ncomp = ", component), colnames(summary_table)), summary_table4)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	422 plot(0,type='n',axes=FALSE,ann=FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	423 grid.table(summary_table5, rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	424
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	425 ### image of the best m/z
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	426 minimumy = min(coord(msidata)[,2])
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	427 maximumy = max(coord(msidata)[,2])
7 6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 4 diff changeset	428 print(image(msidata, mz = topFeatures(msidata.opls)[1,1], normalize.image = "linear", contrast.enhance = "histogram",smooth.image="gaussian", ylim= c(maximumy+0.2maximumy,minimumy-0.2minimumy), main="best m/z heatmap"))
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	429
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	430 opls_classes = data.frame(msidata.opls\$classes[[1]])
3 585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	431 ## pixel names and coordinates
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	432 ## to remove potential sample names and z dimension, split at comma and take only x and y
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	433 x_coords = unlist(lapply(strsplit(names(pixels(msidata)), ","), `[[`, 1))
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	434 y_coords = unlist(lapply(strsplit(names(pixels(msidata)), ","), `[[`, 2))
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	435 x_coordinates = gsub("x = ","",x_coords)
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	436 y_coordinates = gsub(" y = ","",y_coords)
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	437 pixel_names = paste0("xy_", x_coordinates, "_", y_coordinates)
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	438
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	439 opls_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, opls_classes)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	440 colnames(opls_classes2) = c("pixel names", "x", "y","predicted condition")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	441
2 cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	442 ## remove msidata to clean up RAM space
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	443 rm(msidata)
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	444 gc()
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	445
7 6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 4 diff changeset	446 opls_toplabels = topFeatures(msidata.opls, n=Inf)
2 cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	447 opls_toplabels[,4:6] <-round(opls_toplabels[,4:6],6)
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	448 write.table(opls_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	449 write.table(opls_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	450
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	451 ## image with predicted classes
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	452 prediction_df = cbind(coord(msidata.opls)[,1:2], opls_classes)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	453 colnames(prediction_df) = c("x", "y", "predicted_classes")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	454
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	455 prediction_plot = ggplot(prediction_df, aes(x=x, y=y, fill=predicted_classes))+
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	456 geom_tile() +
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	457 coord_fixed()+
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	458 ggtitle("Predicted condition for each pixel")+
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	459 theme_bw()+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	460 theme(
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	461 plot.background = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	462 panel.grid.major = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	463 panel.grid.minor = element_blank())+
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	464 theme(text=element_text(family="ArialMT", face="bold", size=15))+
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	465 theme(legend.position="bottom",legend.direction="vertical")+
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	466 guides(fill=guide_legend(ncol=4,byrow=TRUE))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	467 coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	468 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	469 print(prediction_plot)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	470
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	471 ## optional output as .RData
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	472 #if $output_rdata:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	473 save(msidata.opls, file="$classification_rdata")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	474 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	475 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	476
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	477
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	478 ######################## SSC #############################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	479 #elif str( $type_cond.method_cond.class_method) == "spatialShrunkenCentroids":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	480 print("SSC")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	481
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	482 ######################## SSC - CV #############################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	483 #if str( $type_cond.method_cond.ssc_analysis_cond.ssc_method) == "ssc_cvapply":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	484 print("SSC cv")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	485
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	486 ## set variables for components and number of response groups
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	487 number_groups = length(levels(y_vector))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	488
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	489 ## SSC-cvApply:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	490 msidata.cv.ssc <- cvApply(msidata, .y = y_vector,.fold = fold_vector,.fun = "spatialShrunkenCentroids", r = c($type_cond.method_cond.ssc_r), s = c($type_cond.method_cond.ssc_s), method = "$type_cond.method_cond.ssc_kernel_method")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	491
2 cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	492 ## remove msidata to clean up RAM space
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	493 rm(msidata)
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	494 gc()
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	495
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	496 ## create table with summary
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	497 count = 1
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	498 summary_ssccv = list()
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	499 accuracy_vector = numeric()
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	500 iteration_vector = character()
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	501 for (iteration in names(msidata.cv.ssc@resultData[[1]][,1])){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	502
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	503 summary_iteration = summary(msidata.cv.ssc)\$accuracy[[iteration]]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	504 ## change class of numbers into numeric to round and calculate mean
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	505 summary_iteration2 = round(as.numeric(summary_iteration), digits=2)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	506 summary_matrix = matrix(summary_iteration2, nrow=4, ncol=number_groups)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	507 accuracy_vector[count] = mean(summary_matrix[1,]) ## vector with accuracies to find later maximum for plot
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	508 summary_iteration3 = cbind(rownames(summary_iteration), summary_matrix) ## include rownames in table
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	509 summary_iteration4 = t(summary_iteration3)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	510 summary_iteration5 = cbind(c(iteration, colnames(summary_iteration)), summary_iteration4)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	511 summary_ssccv[[count]] = summary_iteration5
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	512 iteration_vector[count] = unlist(strsplit(iteration, "[,]"))[3]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	513 count = count+1} ## create list with summary table for each component
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	514 summary_ssccv = do.call(rbind, summary_ssccv)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	515 summary_df = as.data.frame(summary_ssccv)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	516 colnames(summary_df) = NULL
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	517
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	518 ## plot to find parameters with highest accuracy
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	519 plot(c($type_cond.method_cond.ssc_s),accuracy_vector[!duplicated(iteration_vector)], type="o",ylab="Mean accuracy", xlab = "Shrinkage parameter (s)", main="Mean accuracy of SSC classification")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	520 best_params = names(msidata.cv.ssc@resultData[[1]][,1])[which.max(accuracy_vector)] ## find parameters with max. accuracy
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	521 r_value = as.numeric(substring(unlist(strsplit(best_params, ","))[1], 4))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	522 s_value = as.numeric(substring(unlist(strsplit(best_params, ","))[3], 5)) ## remove space
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	523 minimumy = min(coord(msidata.cv.ssc)[,2])
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	524 maximumy = max(coord(msidata.cv.ssc)[,2])
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	525 image(msidata.cv.ssc, model = list( r = r_value, s = s_value ), ylim= c(maximumy+0.2maximumy,minimumy-0.2minimumy),layout=c(1,1))
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	526
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	527 #if $type_cond.method_cond.ssc_analysis_cond.write_best_params:
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	528 write.table(r_value, file="$best_r", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	529 write.table(s_value, file="$best_s", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	530 #end if
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	531
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	532 ## print table with summary in pdf
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	533 par(opar)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	534 plot(0,type='n',axes=FALSE,ann=FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	535 title(main="Summary for the different parameters\n", adj=0.5)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	536 ## 20 rows fits in one page:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	537 if (nrow(summary_df)<=20){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	538 grid.table(summary_df, rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	539 }else{
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	540 grid.table(summary_df[1:20,], rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	541 mincount = 21
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	542 maxcount = 40
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	543 for (count20 in 1:(ceiling(nrow(summary_df)/20)-1)){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	544 plot(0,type='n',axes=FALSE,ann=FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	545 if (maxcount <= nrow(summary_df)){
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	546 grid.table(summary_df[mincount:maxcount,], rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	547 mincount = mincount+20
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	548 maxcount = maxcount+20
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	549 }else{### stop last page with last sample otherwise NA in table
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	550 grid.table(summary_df[mincount:nrow(summary_df),], rows= NULL)}
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	551 }
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	552 }
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	553
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	554 ## optional output as .RData
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	555 #if $output_rdata:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	556 save(msidata.cv.ssc, file="$classification_rdata")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	557 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	558
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	559 ######################## SSC -analysis ###########################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	560 #elif str( $type_cond.method_cond.ssc_analysis_cond.ssc_method) == "ssc_analysis":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	561 print("SSC analysis")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	562
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	563 ## set variables for components and number of response groups
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	564 number_groups = length(levels(y_vector))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	565
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	566 ## SSC analysis and plot
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	567 msidata.ssc <- spatialShrunkenCentroids(msidata, y = y_vector,
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	568 r = c($type_cond.method_cond.ssc_r), s = c($type_cond.method_cond.ssc_s), method = "$type_cond.method_cond.ssc_kernel_method")
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	569 plot(msidata.ssc, mode = "tstatistics", model = list("r" = c($type_cond.method_cond.ssc_r), "s" = c($type_cond.method_cond.ssc_s)),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	570 col=hue_pal()(length(levels(msidata.ssc\$classes[[1]]))), lwd=2)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	571
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	572
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	573
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	574 ### summary table SSC
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	575 ##############summary_table = summary(msidata.ssc)
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	576
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	577 ### stop if multiple values for r and s were used as input
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	578 tryCatch(
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	579 {
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	580
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	581 if (length(names(msidata.ssc@resultData))>1)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	582 {
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	583 stop(call.=FALSE)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	584 }
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	585 },
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	586 error=function(cond) {
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	587 ## in case user used multiple inputs for r or s stop - this is only possible in cv apply
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	588 message("Error during SSC training")
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	589 message("Possible problem: multiple values for r or s selected - this is only possible in cvapply but not for spatial shrunken centroid analysis)")
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	590 stop(call.=FALSE)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	591 }
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	592 )
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	593
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	594 summary_table = summary(msidata.ssc)\$accuracy[[names(msidata.ssc@resultData)]]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	595 summary_table2 = round(as.numeric(summary_table), digits=2)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	596 summary_matrix = matrix(summary_table2, nrow=4, ncol=number_groups)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	597 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	598 summary_table4 = t(summary_table3)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	599 summary_table5 = cbind(c(names(msidata.ssc@resultData),colnames(summary_table)), summary_table4)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	600 plot(0,type='n',axes=FALSE,ann=FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	601 grid.table(summary_table5, rows= NULL)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	602
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	603 ### image of the best m/z
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	604 minimumy = min(coord(msidata)[,2])
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	605 maximumy = max(coord(msidata)[,2])
7 6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 4 diff changeset	606 print(image(msidata, mz = topFeatures(msidata.ssc)[1,1], normalize.image = "linear", contrast.enhance = "histogram",smooth.image="gaussian", ylim= c(maximumy+0.2maximumy,minimumy-0.2minimumy), main="best m/z heatmap"))
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	607
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	608 ## m/z and pixel information output
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	609 ssc_classes = data.frame(msidata.ssc\$classes[[1]])
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	610 ssc_probabilities = data.frame(msidata.ssc\$probabilities[[1]])
3 585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	611
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	612 ## pixel names and coordinates
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	613 ## to remove potential sample names and z dimension, split at comma and take only x and y
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	614 x_coords = unlist(lapply(strsplit(names(pixels(msidata)), ","), `[[`, 1))
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	615 y_coords = unlist(lapply(strsplit(names(pixels(msidata)), ","), `[[`, 2))
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	616 x_coordinates = gsub("x = ","",x_coords)
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	617 y_coordinates = gsub(" y = ","",y_coords)
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	618 pixel_names = paste0("xy_", x_coordinates, "_", y_coordinates)
585ef27873c9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2 galaxyp parents: 2 diff changeset	619
2 cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	620
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	621 ## remove msidata to clean up RAM space
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	622 rm(msidata)
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	623 gc()
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	624
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	625 ssc_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, ssc_classes, ssc_probabilities)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	626 colnames(ssc_classes2) = c("pixel names", "x", "y","predicted condition", levels(msidata.ssc\$classes[[1]]))
7 6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 4 diff changeset	627 ssc_toplabels = topFeatures(msidata.ssc, n=Inf)
2 cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	628 ssc_toplabels[,6:9] <-round(ssc_toplabels[,6:9],6)
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	629 write.table(ssc_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	630 write.table(ssc_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	631
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	632 image(msidata.ssc, model=list(r = c($type_cond.method_cond.ssc_r), s = c($type_cond.method_cond.ssc_s)),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	633 col=hue_pal()(length(levels(msidata.ssc\$classes[[1]]))), mode="classes", layout=c(1,1), main="Class Prediction")
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	634 image(msidata.ssc, model=list(r = c($type_cond.method_cond.ssc_r), s = c($type_cond.method_cond.ssc_s)),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	635 col=hue_pal()(length(levels(msidata.ssc\$classes[[1]]))), mode="probabilities", layout=c(1,1), main="Class probabilities")
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	636
9 24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	637
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	638 ## image with right and wrong classes:
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	639 prediction_df = cbind(coord(msidata.ssc)[,1:2], ssc_classes)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	640 colnames(prediction_df) = c("x", "y", "predicted_classes")
9 24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	641 comparison_df = cbind(prediction_df, y_vector)
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	642 comparison_df\$correct<- ifelse(comparison_df\$predicted_classes==comparison_df\$y_vector, T, F)
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	643 correctness = round(sum(comparison_df\$correct)/length(comparison_df\$correct)*100,2)
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	644
9 24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	645 correctness_plot = ggplot(comparison_df, aes(x=x, y=y, fill=correct))+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	646 geom_tile() +
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	647 coord_fixed()+
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	648 ggtitle(paste0("Correctness of classification: ",correctness, "%"))+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	649 scale_fill_manual(values = c("TRUE" = "orange","FALSE" = "darkblue"))+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	650 theme_bw()+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	651 theme(
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	652 plot.background = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	653 panel.grid.major = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	654 panel.grid.minor = element_blank())+
9 24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	655 theme(text=element_text(family="ArialMT", face="bold", size=15))+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	656 theme(legend.position="bottom",legend.direction="vertical")+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	657 guides(fill=guide_legend(ncol=2,byrow=TRUE))
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	658 ## coord_labels = aggregate(cbind(x,y)~correct, data=comparison_df, mean, na.rm=TRUE, na.action="na.pass")
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	659 ##coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes)
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	660 print(correctness_plot)
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	661
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	662 ## optional output as .RData
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	663 #if $output_rdata:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	664 save(msidata.ssc, file="$classification_rdata")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	665 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	666
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	667 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	668 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	669
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	670
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	671
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	672 ######################## II) Prediction #############################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	673 #############################################################################
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	674
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	675 #elif str($type_cond.type_method) == "prediction":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	676 print("prediction")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	677
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	678 training_data = loadRData("$type_cond.training_result")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	679
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	680 #if str($type_cond.new_y_values_cond.new_y_values) == "new_response":
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	681 print("new response")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	682
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	683 new_y_tabular = read.delim("$type_cond.new_y_values_cond.new_response_file", header = $type_cond.new_y_values_cond.new_tabular_header, stringsAsFactors = FALSE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	684 new_y_input = new_y_tabular[,c($type_cond.new_y_values_cond.column_new_x, $type_cond.new_y_values_cond.column_new_y, $type_cond.new_y_values_cond.column_new_response)]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	685 colnames(new_y_input)[1:2] = c("x", "y")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	686 ## merge with coordinate information of msidata
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	687 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	688 colnames(msidata_coordinates)[3] = "pixel_index"
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	689 merged_response = merge(msidata_coordinates, new_y_input, by=c("x", "y"), all.x=TRUE)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	690 merged_response[is.na(merged_response)] = "NA"
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	691 merged_response = merged_response[order(merged_response\$pixel_index),]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	692 new_y_vector = as.factor(merged_response[,4])
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	693 prediction = predict(training_data,msidata, newy = new_y_vector)
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	694
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	695 ## Summary table prediction
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	696 summary_table = summary(prediction)\$accuracy[[names(prediction@resultData)]]
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	697 summary_table2 = round(as.numeric(summary_table), digits=2)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	698 summary_matrix = matrix(summary_table2, nrow=4, ncol=ncol(summary_table))
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	699 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	700 summary_table4 = t(summary_table3)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	701 summary_table5 = cbind(c(names(prediction@resultData),colnames(summary_table)), summary_table4)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	702 plot(0,type='n',axes=FALSE,ann=FALSE)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	703 grid.table(summary_table5, rows= NULL)
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	704
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	705 #else
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	706 prediction = predict(training_data,msidata)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	707 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	708
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	709 ## m/z and pixel information output
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	710 predicted_classes = data.frame(prediction\$classes[[1]])
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	711 pixel_names = gsub(", y = ", "_", names(pixels(msidata)))
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	712 pixel_names = gsub(" = ", "y_", pixel_names)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	713 x_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,2]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	714 y_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,3]
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	715 predicted_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, predicted_classes)
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	716 colnames(predicted_classes2) = c("pixel names", "x", "y","predicted condition")
7 6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 4 diff changeset	717 predicted_toplabels = topFeatures(prediction, n=Inf)
2 cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	718 if (colnames(predicted_toplabels)[4] == "coefficients"){
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	719 predicted_toplabels[,4:6] <-round(predicted_toplabels[,4:6],5)
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	720 }else{
cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	721 predicted_toplabels[,6:9] <-round(predicted_toplabels[,6:9],5)}
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	722
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	723 ##predicted classes
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	724 prediction_df = cbind(coord(prediction)[,1:2], predicted_classes)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	725 colnames(prediction_df) = c("x", "y", "predicted_classes")
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	726
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	727 #if str($type_cond.classification_type) == "SSC_classifier":
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	728 ## this seems to work only for SSC, therefore overwrite tables
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	729 predicted_probabilities = data.frame(prediction\$probabilities[[1]])
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	730 predicted_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, predicted_classes, predicted_probabilities)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	731 colnames(predicted_classes2) = c("pixel names", "x", "y","predicted condition", levels(prediction\$classes[[1]]))
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	732 ## also image modes are specific to SSC
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	733 image(prediction, mode="classes", layout=c(1,1), main="Class", col=hue_pal()(length(unique(prediction\$classes[[1]]))))
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	734 image(prediction, mode="probabilities", layout=c(1,1), main="Class probabilities", col=hue_pal()(length(unique(prediction\$classes[[1]]))))
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	735
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	736 #else
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	737
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	738 prediction_plot = ggplot(prediction_df, aes(x=x, y=y, fill=predicted_classes))+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	739 geom_tile()+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	740 coord_fixed()+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	741 ggtitle("Predicted condition for each spectrum")+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	742 theme_bw()+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	743 theme(
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	744 plot.background = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	745 panel.grid.major = element_blank(),
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	746 panel.grid.minor = element_blank())+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	747 theme(text=element_text(family="ArialMT", face="bold", size=15))+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	748 theme(legend.position="bottom", legend.direction="vertical")+
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	749 guides(fill=guide_legend(ncol=4, byrow=TRUE))
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	750 coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass")
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	751 coord_labels\$file_number = gsub( "_.*§", "", coord_labels\$predicted_classes)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	752 print(prediction_plot)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	753 #end if
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	754
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	755 write.table(predicted_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	756 write.table(predicted_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	757
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	758
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	759
9 24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	760
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	761 #if str($type_cond.new_y_values_cond.new_y_values) == "new_response":
9 24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	762 ## image with right and wrong classes:
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	763
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	764 comparison_df = cbind(prediction_df, new_y_vector)
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	765 comparison_df\$correct<- ifelse(comparison_df\$predicted_classes==comparison_df\$new_y_vector, T, F)
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	766 correctness = round(sum(comparison_df\$correct)/length(comparison_df\$correct)*100,2)
9 24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	767
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	768 correctness_plot = ggplot(comparison_df, aes(x=x, y=y, fill=correct))+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	769 geom_tile()+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	770 scale_fill_manual(values = c("TRUE" = "orange","FALSE" = "darkblue"))+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	771 coord_fixed()+
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	772 ggtitle(paste0("Correctness of classification: ",correctness, "%"))+
9 24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	773 theme_bw()+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	774 theme(text=element_text(family="ArialMT", face="bold", size=15))+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	775 theme(legend.position="bottom",legend.direction="vertical")+
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	776 guides(fill=guide_legend(ncol=2,byrow=TRUE))
24c000517173 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" galaxyp parents: 8 diff changeset	777 print(correctness_plot)
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	778 #end if
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	779
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	780 ## optional output as .RData
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	781 #if $output_rdata:
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	782 msidata = prediction
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	783 save(msidata, file="$classification_rdata")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	784 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	785
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	786 #end if
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	787
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	788 dev.off()
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	789
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	790 }else{
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	791 print("Inputfile has no intensities > 0 or contains NA values")
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	792 dev.off()
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	793 }
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	794
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	795
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	796 ]]></configfile>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	797 </configfiles>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	798 <inputs>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	799 <expand macro="reading_msidata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	800 <conditional name="type_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	801 <param name="type_method" type="select" label="Analysis step to perform">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	802 <option value="training" selected="True">training</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	803 <option value="prediction">prediction</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	804 </param>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	805 <when value="training">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	806
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	807 <param name="annotation_file" type="data" format="tabular" label="Load tabular file with pixel coordinates and their classes"
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	808 help="Three or four columns: x values, y values, response values, optionally fold values"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	809 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	810 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	811 <param name="column_response" data_ref="annotation_file" label="Column with response (condition) values" type="data_column" help="This is the condition (pixel group) which will be classified"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	812 <param name="column_fold" data_ref="annotation_file" optional="True" label="Column with fold values - only neccessary for cvapply" type="data_column" help="Each fold must contain pixels of all response groups and is used for cross validation"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	813 <param name="tabular_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	814
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	815 <conditional name="method_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	816 <param name="class_method" type="select" label="Select the method for classification">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	817 <option value="PLS" selected="True">PLS-DA</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	818 <option value="OPLS">OPLS-DA</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	819 <option value="spatialShrunkenCentroids">spatial shrunken centroids</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	820 </param>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	821 <when value="PLS">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	822
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	823 <conditional name="analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	824 <param name="PLS_method" type="select" label="Crossvalidation or analysis">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	825 <option value="cvapply" selected="True">cvApply</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	826 <option value="PLS_analysis">PLS-DA analysis</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	827 </param>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	828 <when value="cvapply">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	829 <param name="plscv_comp" type="text" value="1:2"
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	830 label="The number of PLS-DA components" help="For cvapply multiple values are allowed (e.g. 1,2,3 or 2:5). Mininum is 1.">
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	831 <expand macro="sanitizer_multiple_digits"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	832 </param>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	833 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	834 <when value="PLS_analysis">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	835 <param name="pls_comp" type="integer" value="5"
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	836 label="The optimal number of PLS-DA components as indicated by cross-validations (minimum is 1)" help="Run cvApply first to optain optimal number of PLS-DA components"/>
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	837 <param name="pls_scale" type="boolean" label="Data scaling" truevalue="TRUE" falsevalue="FALSE"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	838 <param name="pls_toplabels" type="integer" value="100"
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	839 label="Number of toplabels (m/z features) which should be written in tabular output"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	840 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	841 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	842 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	843
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	844 <when value="OPLS">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	845
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	846 <conditional name="opls_analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	847 <param name="opls_method" type="select" label="Analysis step to perform">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	848 <option value="opls_cvapply" selected="True">cvApply</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	849 <option value="opls_analysis">OPLS-DA analysis</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	850 </param>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	851
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	852 <when value="opls_cvapply">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	853 <param name="opls_cvcomp" type="text" value="1:2"
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	854 label="The number of OPLS-DA components" help="For cvapply multiple values are allowed (e.g. 1,2,3 or 2:5). Minimum is 1.">
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	855 <expand macro="sanitizer_multiple_digits"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	856 </param>
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	857 <!--param name="xnew_cv" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Keep new matrix"/-->
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	858 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	859
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	860 <when value="opls_analysis">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	861 <param name="opls_comp" type="integer" value="5"
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	862 label="The optimal number of OPLS-DA components as indicated by cross-validations (minimum is 1)" help="Run cvApply first to optain optimal number of OPLS-DA components"/>
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	863 <!--param name="xnew" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Keep new matrix"/-->
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	864 <param name="opls_scale" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Data scaling"/>
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	865 <!--param name="opls_toplabels" type="integer" value="100"
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	866 label="Number of toplabels (m/z features) which should be written in tabular output"/-->
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	867 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	868 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	869 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	870
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	871 <when value="spatialShrunkenCentroids">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	872 <conditional name="ssc_analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	873 <param name="ssc_method" type="select" label="Analysis step to perform">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	874 <option value="ssc_cvapply" selected="True">cvApply</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	875 <option value="ssc_analysis">spatial shrunken centroids analysis</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	876 </param>
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	877 <when value="ssc_cvapply">
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	878 <param name="write_best_params" type="boolean" label="Write out best r and s values" help="Can be used to generate automatic classification workflow"/>
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	879 </when>
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	880 <when value="ssc_analysis">
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	881 <!--param name="ssc_toplabels" type="integer" value="100"
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	882 label="Number of toplabels (m/z features) which should be written in tabular output"/-->
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	883 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	884 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	885 <param name="ssc_r" type="text" value="2"
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	886 label="The spatial neighborhood radius of nearby pixels to consider (r)" help="For cvapply multiple values are allowed (e.g. 0,1,2,3 or 2:5)">
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	887 <expand macro="sanitizer_multiple_digits"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	888 </param>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	889 <param name="ssc_s" type="text" value="2"
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	890 label="The sparsity thresholding parameter by which to shrink the t-statistics (s)." help="For cvapply multiple values are allowed (e.g. 0,1,2 or 2:5)">
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	891 <expand macro="sanitizer_multiple_digits"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	892 </param>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	893 <param name="ssc_kernel_method" type="select" display="radio" label = "The method to use to calculate the spatial smoothing kernels for the embedding. The 'gaussian' method refers to spatially-aware (SA) weights, and 'adaptive' refers to spatially-aware structurally-adaptive (SASA) weights">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	894 <option value="gaussian">gaussian</option>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	895 <option value="adaptive" selected="True">adaptive</option>
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	896 </param>
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	897 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	898 </conditional>
8 277dc652246e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" galaxyp parents: 7 diff changeset	899
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	900 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	901
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	902 <when value="prediction">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	903 <param name="training_result" type="data" format="rdata" label="Result from previous classification training"/>
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	904 <!--param name="predicted_toplabels" type="integer" value="100"
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	905 label="Number of toplabels (m/z features) which should be written in tabular output"/-->
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	906 <param name="classification_type" type="select" display="radio" optional="False" label="Which classification method was used">
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	907 <option value="PLS_classifier" selected="True" >PLS classifier</option>
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	908 <option value="OPLS_classifier">OPLS classifier</option>
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	909 <option value="SSC_classifier">SSC_classifier</option>
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	910 </param>
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	911 <conditional name="new_y_values_cond">
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	912 <param name="new_y_values" type="select" label="Load annotations (optional, but allows accuracy calculations)">
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	913 <option value="no_new_response" selected="True">no</option>
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	914 <option value="new_response">use annotations</option>
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	915 </param>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	916 <when value="no_new_response"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	917 <when value="new_response">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	918 <param name="new_response_file" type="data" format="tabular" label="Load tabular file with pixel coordinates and the new response"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	919 <param name="column_new_x" data_ref="new_response_file" label="Column with x values" type="data_column"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	920 <param name="column_new_y" data_ref="new_response_file" label="Column with y values" type="data_column"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	921 <param name="column_new_response" data_ref="new_response_file" label="Column with new response values" type="data_column"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	922 <param name="new_tabular_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	923 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	924 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	925 </when>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	926 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	927 <param name="output_rdata" type="boolean" label="Results as .RData output" help="Can be used to generate a classification prediction on new data"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	928 </inputs>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	929 <outputs>
2 cbc7e53518ce planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 galaxyp parents: 1 diff changeset	930 <data format="pdf" name="classification_images" from_work_dir="classificationpdf.pdf" label = "${tool.name} on ${on_string}: results"/>
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	931 <data format="tabular" name="mzfeatures" label="${tool.name} on ${on_string}: features"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	932 <data format="tabular" name="pixeloutput" label="${tool.name} on ${on_string}: pixels"/>
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	933 <data format="txt" name="best_r" label="${tool.name} on ${on_string}:best r">
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	934 <filter>type_cond['type_method'] == 'training' and type_cond['method_cond']['class_method'] == 'spatialShrunkenCentroids' and type_cond['method_cond']['ssc_analysis_cond']['ssc_method'] == 'ssc_cvapply' and type_cond['method_cond']['ssc_analysis_cond']['write_best_params']</filter>
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	935 </data>
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	936 <data format="txt" name="best_s" label="${tool.name} on ${on_string}:best s">
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	937 <filter>type_cond['type_method'] == 'training' and type_cond['method_cond']['class_method'] == 'spatialShrunkenCentroids' and type_cond['method_cond']['ssc_analysis_cond']['ssc_method'] == 'ssc_cvapply' and type_cond['method_cond']['ssc_analysis_cond']['write_best_params']</filter>
ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	938 </data>
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	939 <data format="rdata" name="classification_rdata" label="${tool.name} on ${on_string}: results.RData">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	940 <filter>output_rdata</filter>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	941 </data>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	942 </outputs>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	943 <tests>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	944 <test expect_num_outputs="3">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	945 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	946 <conditional name="type_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	947 <param name="type_method" value="training"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	948 <param name="annotation_file" value= "pixel_annotation_file1.tabular" ftype="tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	949 <param name="column_x" value="1"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	950 <param name="column_y" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	951 <param name="column_response" value="4"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	952 <param name="column_fold" value="3"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	953 <param name="tabular_header" value="False"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	954 <conditional name="method_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	955 <param name="class_method" value="PLS"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	956 <conditional name="analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	957 <param name="PLS_method" value="cvapply"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	958 <param name="plscv_comp" value="2:4"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	959 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	960 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	961 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	962 <output name="mzfeatures" file="features_test1.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	963 <output name="pixeloutput" file="pixels_test1.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	964 <output name="classification_images" file="test1.pdf" compare="sim_size" delta="2000"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	965 </test>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	966
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	967 <test expect_num_outputs="4">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	968 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	969 <conditional name="type_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	970 <param name="type_method" value="training"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	971 <param name="annotation_file" value= "pixel_annotation_file1.tabular" ftype="tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	972 <param name="column_x" value="1"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	973 <param name="column_y" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	974 <param name="column_response" value="4"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	975 <param name="tabular_header" value="False"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	976 <conditional name="method_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	977 <param name="class_method" value="PLS"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	978 <conditional name="analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	979 <param name="PLS_method" value="PLS_analysis"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	980 <param name="pls_comp" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	981 <param name="pls_scale" value="TRUE"/>
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	982 <!--param name="pls_toplabels" value="100"/-->
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	983 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	984 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	985 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	986 <param name="output_rdata" value="True"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	987 <output name="mzfeatures" file="features_test2.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	988 <output name="pixeloutput" file="pixels_test2.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	989 <output name="classification_images" file="test2.pdf" compare="sim_size"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	990 <output name="classification_rdata" file="test2.rdata" compare="sim_size"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	991 </test>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	992
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	993 <test expect_num_outputs="3">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	994 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	995 <conditional name="type_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	996 <param name="type_method" value="training"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	997 <param name="annotation_file" value= "random_factors.tabular" ftype="tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	998 <param name="column_x" value="1"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	999 <param name="column_y" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1000 <param name="column_response" value="4"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1001 <param name="column_fold" value="3"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1002 <param name="tabular_header" value="False"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1003 <conditional name="method_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1004 <param name="class_method" value="OPLS"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1005 <conditional name="opls_analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1006 <param name="opls_method" value="opls_cvapply"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1007 <param name="opls_cvcomp" value="1:2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1008 <param name="xnew_cv" value="FALSE"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1009 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1010 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1011 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1012 <output name="mzfeatures" file="features_test3.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1013 <output name="pixeloutput" file="pixels_test3.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1014 <output name="classification_images" file="test3.pdf" compare="sim_size"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1015 </test>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1016
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1017 <test expect_num_outputs="4">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1018 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1019 <conditional name="type_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1020 <param name="type_method" value="training"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1021 <param name="annotation_file" value= "random_factors.tabular" ftype="tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1022 <param name="column_x" value="1"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1023 <param name="column_y" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1024 <param name="column_response" value="4"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1025 <param name="tabular_header" value="False"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1026 <conditional name="method_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1027 <param name="class_method" value="OPLS"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1028 <conditional name="opls_analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1029 <param name="opls_method" value="opls_analysis"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1030 <param name="opls_comp" value="3"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1031 <param name="xnew" value="FALSE"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1032 <param name="opls_scale" value="FALSE"/>
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1033 <!--param name="opls_toplabels" value="100"/-->
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1034 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1035 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1036 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1037 <param name="output_rdata" value="True"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1038 <output name="mzfeatures" file="features_test4.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1039 <output name="pixeloutput" file="pixels_test4.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1040 <output name="classification_images" file="test4.pdf" compare="sim_size"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1041 <output name="classification_rdata" file="test4.rdata" compare="sim_size"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1042 </test>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1043
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1044 <test expect_num_outputs="3">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1045 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1046 <conditional name="type_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1047 <param name="type_method" value="training"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1048 <param name="annotation_file" value= "pixel_annotation_file1.tabular" ftype="tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1049 <param name="column_x" value="1"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1050 <param name="column_y" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1051 <param name="column_response" value="3"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1052 <param name="column_fold" value="4"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1053 <param name="tabular_header" value="False"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1054 <conditional name="method_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1055 <param name="class_method" value="spatialShrunkenCentroids"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1056 <conditional name="ssc_analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1057 <param name="ssc_method" value="ssc_cvapply"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1058 <param name="ssc_r" value="1:2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1059 <param name="ssc_s" value="2:3"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1060 <param name="ssc_kernel_method" value="adaptive"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1061 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1062 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1063 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1064 <output name="mzfeatures" file="features_test5.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1065 <output name="pixeloutput" file="pixels_test5.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1066 <output name="classification_images" file="test5.pdf" compare="sim_size"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1067 </test>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1068
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1069 <test expect_num_outputs="4">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1070 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1071 <conditional name="type_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1072 <param name="type_method" value="training"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1073 <param name="annotation_file" value= "random_factors.tabular" ftype="tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1074 <param name="column_x" value="1"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1075 <param name="column_y" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1076 <param name="column_response" value="4"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1077 <conditional name="method_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1078 <param name="class_method" value="spatialShrunkenCentroids"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1079 <conditional name="ssc_analysis_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1080 <param name="ssc_method" value="ssc_analysis"/>
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1081 <!--param name="ssc_toplabels" value="20"/-->
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1082 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1083 <param name="ssc_r" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1084 <param name="ssc_s" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1085 <param name="ssc_kernel_method" value="adaptive"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1086 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1087 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1088 <param name="output_rdata" value="True"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1089 <output name="mzfeatures" file="features_test6.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1090 <output name="pixeloutput" file="pixels_test6.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1091 <output name="classification_images" file="test6.pdf" compare="sim_size"/>
7 6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 4 diff changeset	1092 <output name="classification_rdata" file="test6.rdata" compare="sim_size" delta="15000"/>
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1093 </test>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1094
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1095 <test expect_num_outputs="4">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1096 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1097 <conditional name="type_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1098 <param name="type_method" value="prediction"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1099 <param name="training_result" value="test2.rdata" ftype="rdata"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1100 <conditional name="new_y_values_cond">
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1101 <param name="new_y_values" value="new_response"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1102 <param name="new_response_file" value="pixel_annotation_file1.tabular" ftype="tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1103 <param name="column_new_x" value="1"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1104 <param name="column_new_y" value="2"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1105 <param name="column_new_response" value="4"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1106 <param name="new_tabular_header" value="False"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1107 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1108 </conditional>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1109 <param name="output_rdata" value="True"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1110 <output name="mzfeatures" file="features_test7.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1111 <output name="pixeloutput" file="pixels_test7.tabular"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1112 <output name="classification_images" file="test7.pdf" compare="sim_size"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1113 <output name="classification_rdata" file="test7.rdata" compare="sim_size" />
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1114 </test>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1115 </tests>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1116 <help>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1117 <![CDATA[
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1118
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1119
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1120 @CARDINAL_DESCRIPTION@
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1121
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1122 -----
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1123
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1124 This tool provides three different Cardinal functions for supervised classification of mass-spectrometry imaging data.
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1125
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1126 @MSIDATA_INPUT_DESCRIPTION@
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1127 - NA intensities are not allowed
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1128 - duplicated coordinates will be removed
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1129
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1130 - For training: tabular file with condition and fold for each pixel: Two columns for pixel coordinates (x and y values); one column with the condition for the pixel, which will be used for classification; for the cross validation (cvapply) another column with a fold is necessary, each fold must contain pixels of all response groups and is used for cross validation. Condition and fold columns are treated as factor to perform discriminant analysis (also when numeric values are provided).
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1131
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1132 ::
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1133
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1134 x_coord y_coord condition fold
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1135 1 1 A f1
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1136 2 1 A f2
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1137 3 1 A f3
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1138 1 2 B f1
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1139 2 2 B f2
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1140 3 2 B f3
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1141 ...
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1142 ...
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1143
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1144
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1145 - For prediction: RData output from previous classification run is needed as input, optionally new response values can be loaded with a tabular file containing x values, y values and the response
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1146
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1147
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1148 Options
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1149
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1150 - PLS-DA: partial least square discriminant analysis
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1151 - O-PLS-DA: Orthogonal partial least squares discriminant analysis
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1152 - Spatial shrunken centroids (more details in `Bemis et al. <https://doi.org/10.1074/mcp.O115.053918>`_)
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1153 - training and prediction
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1154
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1155 - training can be done with cvapply that uses cross validation to find the best value for s, this requires not only a condition for each spectrum but also a fold (each fold should contain spectra of all conditions)
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	1156 - training with the best value for r and s gives the top m/z features for each condition and the predicted classification group for each spectrum
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1157 - training result can be saved as RData file that can be reused for prediction of further samples
14 ece627528a78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty" galaxyp parents: 9 diff changeset	1158 - prediction can calculate accuracies when the annotations are known and provided
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1159
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1160
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1161 .. image:: $PATH_TO_IMAGES/classification_overview.png
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1162 :width: 1000
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1163 :height: 465
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1164
47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1165
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1166
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1167 Tips
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1168
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1169 - The classification function will only run on files with valid intensity values (NA are not allowed)
4 47fc5b518ffc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d galaxyp parents: 3 diff changeset	1170 - Only a single input file is accepted, several files have to be combined previously, for example with the MSI combine tool.
0 2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1171
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1172
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1173 Output
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1174
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1175 - Pdf with the heatmaps and plots for the classification
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1176 - Tabular file with information on m/z features and pixels: toplabels/classes
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1177 - Optional: RData output that can be used to predict new data or to explore the results more deeply with the Cardinal package in R
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1178
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1179 ]]>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1180 </help>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1181 <expand macro="citations"/>
2fdbbb1be2b0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415 galaxyp parents: diff changeset	1182 </tool>
7 6f4c34f8d5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" galaxyp parents: 4 diff changeset	1183

Mercurial > repos > galaxyp > cardinal_classification

annotate classification.xml @ 14:ece627528a78 draft