# HG changeset patch
# User galaxyp
# Date 1550244208 18000
# Node ID 3642ed221eb2d84b5a331dceebf8be53bccbb8c1
# Parent 1d9931768896c48f1b4df3ca84c5d04e51bc771f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
diff -r 1d9931768896 -r 3642ed221eb2 macros.xml
--- a/macros.xml Thu Oct 25 07:30:24 2018 -0400
+++ b/macros.xml Fri Feb 15 10:23:28 2019 -0500
@@ -69,25 +69,92 @@
## Range y coordinates
minimumy = min(coord(msidata)[,2])
maximumy = max(coord(msidata)[,2])
+
+
+ properties = c("Number of m/z features",
+ "Range of m/z values",
+ "Number of pixels",
+ "Range of x coordinates",
+ "Range of y coordinates")
+
+ values = c(paste0(maxfeatures),
+ paste0(minmz, " - ", maxmz),
+ paste0(pixelcount),
+ paste0(minimumx, " - ", maximumx),
+ paste0(minimumy, " - ", maximumy))
+
+ property_df = data.frame(properties, values)
+ ]]>
+
+
+
+ 0, for if conditions
npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)
+ ## Number of NA in spectra matrix
+ NAcount = sum(is.na(spectra(msidata)[]))
+ ## Number of NA in spectra matrix
+ infcount = sum(is.infinite(spectra(msidata)[]))
properties = c("Number of m/z features",
"Range of m/z values",
"Number of pixels",
"Range of x coordinates",
"Range of y coordinates",
- "Range of intensities")
+ "Range of intensities",
+ "Number of NA intensities",
+ "Number of Inf intensities")
values = c(paste0(maxfeatures),
paste0(minmz, " - ", maxmz),
paste0(pixelcount),
paste0(minimumx, " - ", maximumx),
paste0(minimumy, " - ", maximumy),
- paste0(minint, " - ", maxint))
+ paste0(minint, " - ", maxint),
+ paste0(NAcount),
+ paste0(infcount))
property_df = data.frame(properties, values)
]]>
@@ -144,9 +211,9 @@
-
+ label="MSI data"
+ help="Input file as imzML (composite upload), or Cardinal MSImageSet saved as RData (regular upload)"/>
+
diff -r 1d9931768896 -r 3642ed221eb2 spectra_plots.xml
--- a/spectra_plots.xml Thu Oct 25 07:30:24 2018 -0400
+++ b/spectra_plots.xml Fri Feb 15 10:23:28 2019 -0500
@@ -1,4 +1,4 @@
-
+
mass spectrometry imaging mass spectra plots
@@ -27,6 +27,7 @@
library(ggplot2)
library(scales)
+
@READING_MSIDATA@
@DATA_PROPERTIES@
@@ -52,15 +53,17 @@
## set NA to 0 otherwise plot function will not work
- ##spectra(msidata)[is.na(spectra(msidata)[])] = 0 ## in case of NA values they will be set to zero
+ #if str($processed_cond.processed_file) == "processed":
+ ##processed file needs to be converted into matrix to be able to replace NAs
+ iData(msidata) <- iData(msidata)[]
+ spectra(msidata)[][is.na(spectra(msidata)[])] = 0
+ #else
+ spectra(msidata)[is.na(spectra(msidata))] = 0
+ #end if
- spectra_df = spectra(msidata)[]
- spectra_df[is.na(spectra_df)] = 0
- print(paste0("Number of NA which were converted into 0:",sum(is.na(spectra_df))))
- spectra(msidata) = spectra_df
+## run only if mz and pixels are > 0
-
-if (npeaks > 0){
+if (ncol(msidata)>0 & nrow(msidata) >0){
pixeldf = data.frame(matrix(ncol = 2, nrow=0))
@@ -73,13 +76,21 @@
#for $chosenpixel in $pixel_conditional.repeatpixel:
pixelname = paste0("x = ", $chosenpixel.inputx,", ", "y = ", $chosenpixel.inputy)
- pixelisvalid = as.character(pixelname %in% names(pixels(msidata)))
+
+
+
+ input_pixels = paste($chosenpixel.inputx, $chosenpixel.inputy, sep="_")
+ dataset_pixels = paste(coord(msidata)\$x, coord(msidata)\$y, sep="_")
+
+ pixelisvalid = as.character(input_pixels %in% dataset_pixels)
+
+
+
pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid))
############################# II) control image ####################
if (pixelisvalid == "TRUE"){
- print(pixelisvalid)
image(msidata, mz=$chosenpixel.inputmz, ylim = c(maximumy+(0.2*maximumy),minimumy-1),
colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton,
@@ -188,16 +199,13 @@
key_legend = TRUE
}else{key_legend = FALSE}
- spectra(msidata)[is.na(spectra(msidata)[])] = 0 ## in case of NA values they will be set to zero
plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE)
}else{
- spectra(msidata)[is.na(spectra(msidata)[])] = 0 ## in case of NA values they will be set to zero
plot(msidata, pixel=1:ncol(msidata), key=TRUE)}
##################### II) Sample: plot zoom-in mass spectrum ##########
#if $pixel_conditional.zoomed_sample:
- iData(msidata) <- iData(msidata)[] ## getting back data on disk
#for $token in $pixel_conditional.zoomed_sample:
print("zoomed sample pixels")
@@ -317,7 +325,7 @@
-
+
diff -r 1d9931768896 -r 3642ed221eb2 test-data/112_auto_combined.RData
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/112_auto_combined.ibd
Binary file test-data/112_auto_combined.ibd has changed
diff -r 1d9931768896 -r 3642ed221eb2 test-data/112_auto_combined.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/112_auto_combined.imzml Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,475 @@
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/112_auto_combined.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/112_auto_combined.imzml.txt Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 556
+-rw-r--r-- 1 meli meli 537552 Feb 12 12:25 ibd
+-rw-r--r-- 1 meli meli 25466 Feb 12 12:25 imzml
diff -r 1d9931768896 -r 3642ed221eb2 test-data/112_auto_combined_QC.pdf
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/123_annotation.ibd
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/123_annotation.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_annotation.imzml Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,394 @@
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/123_auto_combined.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_auto_combined.imzml.txt Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 556
+-rw-r--r-- 1 meli meli 537552 Feb 12 12:25 ibd
+-rw-r--r-- 1 meli meli 25466 Feb 12 12:25 imzml
diff -r 1d9931768896 -r 3642ed221eb2 test-data/123_combined.RData
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/123_combined_QC.pdf
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/123_combined_auto.ibd
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/123_combined_auto.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_combined_auto.imzml Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,394 @@
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/123_combined_auto.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_combined_auto.imzml.txt Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 452
+-rw-r--r-- 1 meli meli 436764 Feb 12 00:51 ibd
+-rw-r--r-- 1 meli meli 21166 Feb 12 00:51 imzml
diff -r 1d9931768896 -r 3642ed221eb2 test-data/123_combined_auto.pdf
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/123_combined_auto.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_combined_auto.tabular Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,13 @@
+x y sample_name
+1 1 msidata_1.RData
+1 2 msidata_1.RData
+1 3 msidata_1.RData
+7 1 msidata_2.RData
+8 1 msidata_2.RData
+7 2 msidata_2.RData
+8 2 msidata_2.RData
+7 3 msidata_2.RData
+8 3 msidata_2.RData
+1 9 msidata_3.RData
+1 10 msidata_3.RData
+1 11 msidata_3.RData
diff -r 1d9931768896 -r 3642ed221eb2 test-data/12_combined.RData
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/12_combined_QC.pdf
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/2123_auto_combined.RData
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/2123_auto_combined_QC.pdf
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/Plot_empty_spectra.pdf
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/QC_analyze75.pdf
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/QC_empty_spectra.pdf
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/QC_imzml.pdf
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/QC_rdata.pdf
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/analyze75_filtered2.pdf
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/analyze_filtered.RData
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/analyze_filtered.pdf
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/analyze_filteredoutside.RData
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/analyze_originaloutput.RData
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/analyze_originaloutput2.RData
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/centroids_rdata.pdf
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/cluster_skm.RData
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/features_test2.tabular
--- a/test-data/features_test2.tabular Thu Oct 25 07:30:24 2018 -0400
+++ b/test-data/features_test2.tabular Fri Feb 15 10:23:28 2019 -0500
@@ -1,101 +1,101 @@
mz ncomp column coefficients loadings weights
-938.823120117188 2 A 0.00557062672565914 0.0521481794011343 0.0618954239030616
-938.859741210938 2 A 0.00542130109915229 0.0573197814782043 0.0556644462038001
-952.817016601562 2 A 0.00540658997062797 0.0541785607809472 0.0556957101293819
-980.9658203125 2 A 0.00530572666388636 0.0640830071706491 0.0596133867741965
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/features_test4.tabular
--- a/test-data/features_test4.tabular Thu Oct 25 07:30:24 2018 -0400
+++ b/test-data/features_test4.tabular Fri Feb 15 10:23:28 2019 -0500
@@ -1,101 +1,101 @@
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/features_test6.tabular
--- a/test-data/features_test6.tabular Thu Oct 25 07:30:24 2018 -0400
+++ b/test-data/features_test6.tabular Fri Feb 15 10:23:28 2019 -0500
@@ -1,21 +1,21 @@
mz r k s classes centers tstatistics p.values adj.p.values
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/features_test7.tabular
--- a/test-data/features_test7.tabular Thu Oct 25 07:30:24 2018 -0400
+++ b/test-data/features_test7.tabular Fri Feb 15 10:23:28 2019 -0500
@@ -1,101 +1,101 @@
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--- a/test-data/loadings_pca.tabular Thu Oct 25 07:30:24 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/out3.ibd
Binary file test-data/out3.ibd has changed
diff -r 1d9931768896 -r 3642ed221eb2 test-data/out3.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out3.imzml Fri Feb 15 10:23:28 2019 -0500
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/out3.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out3.imzml.txt Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
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+-rw-r--r-- 1 meli meli 8282 Feb 12 19:18 imzml
diff -r 1d9931768896 -r 3642ed221eb2 test-data/out4.ibd
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/out4.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/out4.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out4.imzml.txt Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
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+-rw-r--r-- 1 meli meli 11141 Feb 12 00:49 imzml
diff -r 1d9931768896 -r 3642ed221eb2 test-data/out5.ibd
Binary file test-data/out5.ibd has changed
diff -r 1d9931768896 -r 3642ed221eb2 test-data/out5.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/out5.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out5.imzml.txt Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
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+-rw-r--r-- 1 meli meli 12508 Feb 12 00:50 imzml
diff -r 1d9931768896 -r 3642ed221eb2 test-data/out6.ibd
Binary file test-data/out6.ibd has changed
diff -r 1d9931768896 -r 3642ed221eb2 test-data/out6.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out6.imzml Fri Feb 15 10:23:28 2019 -0500
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/out6.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out6.imzml.txt Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 164
+-rw-r--r-- 1 meli meli 146896 Feb 12 00:51 ibd
+-rw-r--r-- 1 meli meli 16868 Feb 12 00:51 imzml
diff -r 1d9931768896 -r 3642ed221eb2 test-data/out7.ibd
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/out7.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out7.imzml Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,313 @@
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/out7.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out7.imzml.txt Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 116
+-rw-r--r-- 1 meli meli 95976 Feb 12 00:51 ibd
+-rw-r--r-- 1 meli meli 16846 Feb 12 00:51 imzml
diff -r 1d9931768896 -r 3642ed221eb2 test-data/pca_imzml.pdf
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/pixel_out2.tabular
--- a/test-data/pixel_out2.tabular Thu Oct 25 07:30:24 2018 -0400
+++ b/test-data/pixel_out2.tabular Fri Feb 15 10:23:28 2019 -0500
@@ -1,10 +1,10 @@
-spectra_names x_values y_values pixel_order peaks_per_spectrum spectrum_TIC most_abundant_mz annotation
-xy_1_1 1 1 1 3672 42479 1267.525390625 col1
-xy_2_1 2 1 2 3672 29179 1264.42407226562 col2
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-xy_2_3 2 3 8 3672 33204 1267.48278808594 col2
-xy_3_3 3 3 9 3672 37961 1199.55615234375 col3
+spectra_names x_values y_values pixel_order peaks_per_spectrum median_intensity spectrum_TIC maximum_intensity most_abundant_mz annotation
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/pixel_out3.tabular
--- a/test-data/pixel_out3.tabular Thu Oct 25 07:30:24 2018 -0400
+++ b/test-data/pixel_out3.tabular Fri Feb 15 10:23:28 2019 -0500
@@ -1,10 +1,10 @@
-spectra_names x_values y_values pixel_order peaks_per_spectrum spectrum_TIC most_abundant_mz input m/z count
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessed.rdata
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results1.RData
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results1.ibd
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results1.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results1.imzml Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,313 @@
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results1.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results1.imzml.txt Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
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+-rw-r--r-- 1 meli meli 16714 Feb 12 21:24 imzml
diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results1.pdf
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results1.txt
--- a/test-data/preprocessing_results1.txt Thu Oct 25 07:30:24 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-mz x = 1, y = 1 x = 2, y = 1 x = 3, y = 1 x = 1, y = 2 x = 2, y = 2 x = 3, y = 2 x = 1, y = 3 x = 2, y = 3 x = 3, y = 3
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results2.RData
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results2.ibd
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results2.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results2.imzml Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,394 @@
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results2.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results2.imzml.txt Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results2.pdf
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results2.txt
--- a/test-data/preprocessing_results2.txt Thu Oct 25 07:30:24 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results4.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results4.imzml.txt Fri Feb 15 10:23:28 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 28
+-rw-r--r-- 1 meli meli 6376 Feb 12 21:29 ibd
+-rw-r--r-- 1 meli meli 16801 Feb 12 21:29 imzml
diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results4.pdf
Binary file test-data/preprocessing_results4.pdf has changed
diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results4.txt
--- a/test-data/preprocessing_results4.txt Thu Oct 25 07:30:24 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,160 +0,0 @@
-mz x = 1, y = 1 x = 2, y = 1 x = 3, y = 1 x = 1, y = 2 x = 2, y = 2 x = 3, y = 2 x = 1, y = 3 x = 2, y = 3 x = 3, y = 3
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results5.RData
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results5.pdf
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/preprocessing_results5.txt
--- a/test-data/preprocessing_results5.txt Thu Oct 25 07:30:24 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
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diff -r 1d9931768896 -r 3642ed221eb2 test-data/scores_pca.tabular
--- a/test-data/scores_pca.tabular Thu Oct 25 07:30:24 2018 -0400
+++ b/test-data/scores_pca.tabular Fri Feb 15 10:23:28 2019 -0500
@@ -1,10 +1,10 @@
pixel names x y PC1 PC2
-xy_1_1 1 1 1.00970093989579 0.757987492163095
-xy_2_1 2 1 0.579669229309751 -0.365615195586663
-xy_3_1 3 1 -1.04790449059337 0.831141108678224
-xy_1_2 1 2 3.5004093695087 0.608578545994517
-xy_2_2 2 2 -0.325050824762022 0.275854508943195
-xy_3_2 3 2 -1.31374997886227 0.0192699346592569
-xy_1_3 1 3 -1.46193831394872 -0.0337353199555284
-xy_2_3 2 3 -1.08833133183905 1.16461090511219
-xy_3_3 3 3 0.147195401291175 -3.25809198000829
+xy_1_1 1 1 1.009701 0.757987
+xy_2_1 2 1 0.579669 -0.365615
+xy_3_1 3 1 -1.047904 0.831141
+xy_1_2 1 2 3.500409 0.608579
+xy_2_2 2 2 -0.325051 0.275855
+xy_3_2 3 2 -1.31375 0.01927
+xy_1_3 1 3 -1.461938 -0.033735
+xy_2_3 2 3 -1.088331 1.164611
+xy_3_3 3 3 0.147195 -3.258092
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