# HG changeset patch
# User galaxyp
# Date 1550243796 18000
# Node ID 034885df9b09b5260d5fd2342be3c8b6eb1b1938
# Parent 98d48f081ad9b5fb9c74469168b82a2b43431435
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
diff -r 98d48f081ad9 -r 034885df9b09 macros.xml
--- a/macros.xml Thu Oct 25 07:25:52 2018 -0400
+++ b/macros.xml Fri Feb 15 10:16:36 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 98d48f081ad9 -r 034885df9b09 segmentation.xml
--- a/segmentation.xml Thu Oct 25 07:25:52 2018 -0400
+++ b/segmentation.xml Fri Feb 15 10:16:36 2019 -0500
@@ -1,4 +1,4 @@
-
+
mass spectrometry imaging spatial clustering
macros.xml
@@ -26,13 +26,18 @@
library(gridExtra)
library(lattice)
-@READING_MSIDATA@
-## create full matrix to make processed imzML files compatible with segmentation
-iData(msidata) <- iData(msidata)[]
+@READING_MSIDATA_INRAM@
+
+## to make sure that processed files work as well:
+iData(msidata) = iData(msidata)[]
-@DATA_PROPERTIES@
+## count and print number of NAs, all methods are not compatible with NAs
+print(paste0("Number of NA in dataset: ", sum(is.na(spectra(msidata)[])), " - segmentation does not work with NA values"))
+
+@DATA_PROPERTIES_INRAM@
+
######################################## PDF ###################################
################################################################################
@@ -49,7 +54,7 @@
#############################################################################
grid.table(property_df, rows= NULL)
-if (npeaks > 0)
+if (npeaks > 0 && sum(is.na(spectra(msidata)[]))==0)
{
######################## II) segmentation tools #############################
@@ -81,10 +86,25 @@
component_vector = character()
for (numberofcomponents in 1:$segm_cond.pca_ncomp)
- {component_vector[numberofcomponents]= paste0("PC", numberofcomponents)}
+ {component_vector[numberofcomponents]= paste0("PC", numberofcomponents)}
+
pca_result = PCA(msidata, ncomp=$segm_cond.pca_ncomp, column = component_vector, superpose = FALSE,
method = "$segm_cond.pca_method", scale = $segm_cond.pca_scale, layout = c(ncomp, 1))
+ ## remove msidata to clean up RAM space
+ rm(msidata)
+ gc()
+
+ ### table in pdf file
+ plot(0,type='n',axes=FALSE,ann=FALSE)
+ sd_table = as.data.frame(round(pca_result@resultData\$ncomp\$sdev, digits=2))
+ colnames(sd_table) = "Standard deviation"
+ PC_vector = character()
+ for (PCs in 1:$segm_cond.pca_ncomp){
+ PC_vector[[PCs]] = c(paste0("PC",PCs))}
+ sd_table = cbind(PC_vector, sd_table)
+ colnames(sd_table)[1] = "Principal components"
+ grid.table(sd_table, rows=NULL)
### images in pdf file
print(image(pca_result, main="PCA image", lattice=lattice_input, strip = strip_input, col=colourvector, ylim=c(maximumy+2, minimumy-2)))
for (PCs in 1:$segm_cond.pca_ncomp){
@@ -95,10 +115,10 @@
print(plot(pca_result, column = c(paste0("PC",PCs)),superpose = FALSE))}
### values in tabular files
- pcaloadings = (pca_result@resultData\$ncomp\$loadings) ### loading for each m/z value
+ pcaloadings = formatC(pca_result@resultData\$ncomp\$loadings, format = "e", digits = 6)### loading for each m/z value
pcaloadings2 = cbind(matrix(unlist(strsplit(rownames(pcaloadings), " = ")), ncol=2, byrow=TRUE)[,2], pcaloadings)
colnames(pcaloadings2) = c("mz", colnames(pcaloadings))
- pcascores = (pca_result@resultData\$ncomp\$scores) ### scores for each pixel
+ pcascores = round(pca_result@resultData\$ncomp\$scores, digits=6) ### scores for each pixel
## pixel names and coordinates
## to remove potential sample names and z dimension, split at comma and take only x and y
@@ -125,6 +145,11 @@
##k-means
skm = spatialKMeans(msidata, r=c($segm_cond.kmeans_r), k=c($segm_cond.kmeans_k), method="$segm_cond.kmeans_method")
+
+ ## remove msidata to clean up RAM space
+ rm(msidata)
+ gc()
+
print(image(skm, key=TRUE, main="K-means clustering", lattice=lattice_input, strip=strip_input, col= colourvector, layout=c(1,1), ylim=c(maximumy+2, minimumy-2)))
print(plot(skm, main="K-means plot", lattice=lattice_input, col= colourvector, strip=strip_input, layout=c(1,1)))
@@ -162,6 +187,9 @@
##centroids
ssc = spatialShrunkenCentroids(msidata, r=c($segm_cond.centroids_r), k=c($segm_cond.centroids_k), s=c($segm_cond.centroids_s), method="$segm_cond.centroids_method")
+ ## remove msidata to clean up RAM space
+ rm(msidata)
+ gc()
print(image(ssc, key=TRUE, main="Spatial shrunken centroids", lattice=lattice_input, strip = strip_input, col= colourvector,layout=c(1,1), ylim=c(maximumy+2, minimumy-2)))
print(plot(ssc, main="Spatial shrunken centroids plot", lattice=lattice_input, col= colourvector, strip = strip_input,layout=c(1,1)))
print(plot(ssc, mode = "tstatistics",key = TRUE, lattice=lattice_input, layout = c(1,1), main="t-statistics", col=colourvector))
@@ -274,7 +302,7 @@
-
+
@@ -286,7 +314,7 @@
-
+
@@ -305,7 +333,14 @@
-
+
diff -r 98d48f081ad9 -r 034885df9b09 test-data/112_auto_combined.RData
Binary file test-data/112_auto_combined.RData has changed
diff -r 98d48f081ad9 -r 034885df9b09 test-data/112_auto_combined.ibd
Binary file test-data/112_auto_combined.ibd has changed
diff -r 98d48f081ad9 -r 034885df9b09 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 10:16:36 2019 -0500
@@ -0,0 +1,475 @@
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diff -r 98d48f081ad9 -r 034885df9b09 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 10:16:36 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 98d48f081ad9 -r 034885df9b09 test-data/112_auto_combined_QC.pdf
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/123_annotation.ibd
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/123_annotation.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_annotation.imzml Fri Feb 15 10:16:36 2019 -0500
@@ -0,0 +1,394 @@
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diff -r 98d48f081ad9 -r 034885df9b09 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 10:16:36 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 98d48f081ad9 -r 034885df9b09 test-data/123_combined.RData
Binary file test-data/123_combined.RData has changed
diff -r 98d48f081ad9 -r 034885df9b09 test-data/123_combined_QC.pdf
Binary file test-data/123_combined_QC.pdf has changed
diff -r 98d48f081ad9 -r 034885df9b09 test-data/123_combined_auto.ibd
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diff -r 98d48f081ad9 -r 034885df9b09 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 10:16:36 2019 -0500
@@ -0,0 +1,394 @@
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diff -r 98d48f081ad9 -r 034885df9b09 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 10:16:36 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 98d48f081ad9 -r 034885df9b09 test-data/123_combined_auto.pdf
Binary file test-data/123_combined_auto.pdf has changed
diff -r 98d48f081ad9 -r 034885df9b09 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 10:16:36 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 98d48f081ad9 -r 034885df9b09 test-data/12_combined.RData
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/12_combined_QC.pdf
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/2123_auto_combined.RData
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/2123_auto_combined_QC.pdf
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/Plot_empty_spectra.pdf
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/QC_analyze75.pdf
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/QC_empty_spectra.pdf
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/QC_imzml.pdf
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/QC_rdata.pdf
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/features_test2.tabular
--- a/test-data/features_test2.tabular Thu Oct 25 07:25:52 2018 -0400
+++ b/test-data/features_test2.tabular Fri Feb 15 10:16:36 2019 -0500
@@ -1,101 +1,101 @@
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/features_test4.tabular
--- a/test-data/features_test4.tabular Thu Oct 25 07:25:52 2018 -0400
+++ b/test-data/features_test4.tabular Fri Feb 15 10:16:36 2019 -0500
@@ -1,101 +1,101 @@
mz ncomp column coefficients loadings weights
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/features_test6.tabular
--- a/test-data/features_test6.tabular Thu Oct 25 07:25:52 2018 -0400
+++ b/test-data/features_test6.tabular Fri Feb 15 10:16:36 2019 -0500
@@ -1,21 +1,21 @@
mz r k s classes centers tstatistics p.values adj.p.values
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/features_test7.tabular
--- a/test-data/features_test7.tabular Thu Oct 25 07:25:52 2018 -0400
+++ b/test-data/features_test7.tabular Fri Feb 15 10:16:36 2019 -0500
@@ -1,101 +1,101 @@
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--- a/test-data/loadings_pca.tabular Thu Oct 25 07:25:52 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/out3.ibd
Binary file test-data/out3.ibd has changed
diff -r 98d48f081ad9 -r 034885df9b09 test-data/out3.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/out3.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out3.imzml.txt Fri Feb 15 10:16:36 2019 -0500
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+imzML file:
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+-rw-r--r-- 1 meli meli 8282 Feb 12 19:18 imzml
diff -r 98d48f081ad9 -r 034885df9b09 test-data/out4.ibd
Binary file test-data/out4.ibd has changed
diff -r 98d48f081ad9 -r 034885df9b09 test-data/out4.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/out4.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out4.imzml.txt Fri Feb 15 10:16:36 2019 -0500
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+-rw-r--r-- 1 meli meli 11141 Feb 12 00:49 imzml
diff -r 98d48f081ad9 -r 034885df9b09 test-data/out5.ibd
Binary file test-data/out5.ibd has changed
diff -r 98d48f081ad9 -r 034885df9b09 test-data/out5.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out5.imzml Fri Feb 15 10:16:36 2019 -0500
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/out5.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out5.imzml.txt Fri Feb 15 10:16:36 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 20
+-rw-r--r-- 1 meli meli 380 Feb 12 00:50 ibd
+-rw-r--r-- 1 meli meli 12508 Feb 12 00:50 imzml
diff -r 98d48f081ad9 -r 034885df9b09 test-data/out6.ibd
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/out6.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out6.imzml Fri Feb 15 10:16:36 2019 -0500
@@ -0,0 +1,313 @@
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/out6.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out6.imzml.txt Fri Feb 15 10:16:36 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 98d48f081ad9 -r 034885df9b09 test-data/out7.ibd
Binary file test-data/out7.ibd has changed
diff -r 98d48f081ad9 -r 034885df9b09 test-data/out7.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out7.imzml Fri Feb 15 10:16:36 2019 -0500
@@ -0,0 +1,313 @@
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/out7.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out7.imzml.txt Fri Feb 15 10:16:36 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 98d48f081ad9 -r 034885df9b09 test-data/pca_imzml.pdf
Binary file test-data/pca_imzml.pdf has changed
diff -r 98d48f081ad9 -r 034885df9b09 test-data/pixel_out2.tabular
--- a/test-data/pixel_out2.tabular Thu Oct 25 07:25:52 2018 -0400
+++ b/test-data/pixel_out2.tabular Fri Feb 15 10:16:36 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
-xy_3_1 3 1 3 3672 37005 1267.525390625 col3
-xy_1_2 1 2 4 3672 42306 1264.38171386719 col1
-xy_2_2 2 2 5 3672 30350 1267.525390625 col2
-xy_3_2 3 2 6 3672 35955 1199.55615234375 col3
-xy_1_3 1 3 7 3672 43872 1199.59753417969 col1
-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
+xy_1_1 1 1 1 3672 11 42479 43 1267.525390625 col1
+xy_2_1 2 1 2 3672 8 29179 20 1264.42407226562 col2
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+xy_1_2 1 2 4 3672 11 42306 49 1264.38171386719 col1
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+xy_3_2 3 2 6 3672 9 35955 39 1199.55615234375 col3
+xy_1_3 1 3 7 3672 11 43872 84 1199.59753417969 col1
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/pixel_out3.tabular
--- a/test-data/pixel_out3.tabular Thu Oct 25 07:25:52 2018 -0400
+++ b/test-data/pixel_out3.tabular Fri Feb 15 10:16:36 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
-xy_1_1 1 1 1 241 22.92 329.083343505859 0
-xy_2_1 2 1 2 332 29.26 328.916687011719 0
-xy_3_1 3 1 3 415 24.43 328.916687011719 0
-xy_1_2 1 2 4 343 39.62 329 0
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-xy_3_2 3 2 6 194 10.79 345.083343505859 0
-xy_1_3 1 3 7 308 14.68 328.916687011719 0
-xy_2_3 2 3 8 367 24.87 329 0
-xy_3_3 3 3 9 323 35.18 329.083343505859 0
+spectra_names x_values y_values pixel_order peaks_per_spectrum median_intensity spectrum_TIC maximum_intensity most_abundant_mz m/z count
+xy_1_1 1 1 1 241 0 22.92 2.48 329.083343505859 0
+xy_2_1 2 1 2 332 0 29.26 2.02 328.916687011719 0
+xy_3_1 3 1 3 415 0 24.43 1.43 328.916687011719 0
+xy_1_2 1 2 4 343 0 39.62 2.59 329 0
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/preprocessed.rdata
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/preprocessing_results1.RData
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/preprocessing_results1.ibd
Binary file test-data/preprocessing_results1.ibd has changed
diff -r 98d48f081ad9 -r 034885df9b09 test-data/preprocessing_results1.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results1.imzml Fri Feb 15 10:16:36 2019 -0500
@@ -0,0 +1,313 @@
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diff -r 98d48f081ad9 -r 034885df9b09 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 10:16:36 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 24
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+-rw-r--r-- 1 meli meli 16714 Feb 12 21:24 imzml
diff -r 98d48f081ad9 -r 034885df9b09 test-data/preprocessing_results1.pdf
Binary file test-data/preprocessing_results1.pdf has changed
diff -r 98d48f081ad9 -r 034885df9b09 test-data/preprocessing_results1.txt
--- a/test-data/preprocessing_results1.txt Thu Oct 25 07:25:52 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
-329 8.48069807321137 6.00276368862812 0 0 7.22240715797167 6.68463797360356 0 0 0
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/preprocessing_results2.RData
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/preprocessing_results2.ibd
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/preprocessing_results2.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results2.imzml Fri Feb 15 10:16:36 2019 -0500
@@ -0,0 +1,394 @@
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diff -r 98d48f081ad9 -r 034885df9b09 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 10:16:36 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 80
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+-rw-r--r-- 1 meli meli 21132 Feb 12 21:25 imzml
diff -r 98d48f081ad9 -r 034885df9b09 test-data/preprocessing_results2.pdf
Binary file test-data/preprocessing_results2.pdf has changed
diff -r 98d48f081ad9 -r 034885df9b09 test-data/preprocessing_results2.txt
--- a/test-data/preprocessing_results2.txt Thu Oct 25 07:25:52 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,297 +0,0 @@
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diff -r 98d48f081ad9 -r 034885df9b09 test-data/preprocessing_results4.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results4.imzml Fri Feb 15 10:16:36 2019 -0500
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diff -r 98d48f081ad9 -r 034885df9b09 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 10:16:36 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 98d48f081ad9 -r 034885df9b09 test-data/preprocessing_results4.pdf
Binary file test-data/preprocessing_results4.pdf has changed
diff -r 98d48f081ad9 -r 034885df9b09 test-data/preprocessing_results4.txt
--- a/test-data/preprocessing_results4.txt Thu Oct 25 07:25:52 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 98d48f081ad9 -r 034885df9b09 test-data/preprocessing_results5.RData
Binary file test-data/preprocessing_results5.RData has changed
diff -r 98d48f081ad9 -r 034885df9b09 test-data/preprocessing_results5.pdf
Binary file test-data/preprocessing_results5.pdf has changed
diff -r 98d48f081ad9 -r 034885df9b09 test-data/preprocessing_results5.txt
--- a/test-data/preprocessing_results5.txt Thu Oct 25 07:25:52 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
- 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 98d48f081ad9 -r 034885df9b09 test-data/scores_pca.tabular
--- a/test-data/scores_pca.tabular Thu Oct 25 07:25:52 2018 -0400
+++ b/test-data/scores_pca.tabular Fri Feb 15 10:16:36 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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