| Previous changeset 0:0c1a9b68f436 (2018-02-24) Next changeset 2:f66c5789deac (2018-03-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a |
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modified:
segmentation_tool.xml test-data/centroids_imzml.pdf test-data/kmeans_imzml.pdf test-data/pca_imzml.pdf |
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added:
test-data/classes_ssc.tabular test-data/cluster_skm.tabular test-data/loadings_pca.tabular test-data/scores_pca.tabular test-data/toplabels_skm.tabular test-data/toplabels_ssc.tabular |
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removed:
test-data/classes_results1.txt test-data/cluster_results1.txt test-data/pcaloadings_results1.txt test-data/pcascores_results1.txt test-data/toplabels_results1.txt |
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| diff -r 0c1a9b68f436 -r d4158c9955ea segmentation_tool.xml --- a/segmentation_tool.xml Sat Feb 24 13:51:32 2018 -0500 +++ b/segmentation_tool.xml Thu Mar 01 08:26:19 2018 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="mass_spectrometry_imaging_segmentations" name="MSI segmentation" version="1.7.0"> +<tool id="mass_spectrometry_imaging_segmentations" name="MSI segmentation" version="1.7.0.1"> <description>tool for spatial clustering</description> <requirements> <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement> @@ -40,9 +40,9 @@ ## Read MALDI Imaging dataset #if $infile.ext == 'imzml' - msidata <- readMSIData('infile.imzML') + msidata = readMSIData('infile.imzML') #elif $infile.ext == 'analyze75' - msidata <- readMSIData('infile.hdr') + msidata = readMSIData('infile.hdr') #else load('infile.RData') #end if @@ -177,10 +177,10 @@ component_vector = character() for (numberofcomponents in 1:$segm_cond.pca_ncomp) {component_vector[numberofcomponents]= paste0("PC", numberofcomponents)} - pca <- PCA(msidata, ncomp=$segm_cond.pca_ncomp, column = component_vector, superpose = FALSE, + pca = PCA(msidata, ncomp=$segm_cond.pca_ncomp, column = component_vector, superpose = FALSE, method = "$segm_cond.pca_method", scale = $segm_cond.pca_scale, layout = c(ncomp, 1)) - print(image(pca, main="PCA image", lattice=TRUE, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), contrast.enhance = "$segm_cond.pca_imagecontrast", smooth.image = "$segm_cond.pca_imagesmoothing", col=colourvector)) + print(image(pca, main="PCA image", lattice=TRUE, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), contrast.enhance = "$segm_cond.pca_imagecontrast", smooth.image = "$segm_cond.pca_imagesmoothing", col=colourvector, ylim=c(maximumy+2, 0))) print(plot(pca, main="PCA plot", lattice=TRUE, col= colourvector, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)))) @@ -194,8 +194,8 @@ print('kmeans') ##k-means - skm <- spatialKMeans(msidata, r=$segm_cond.kmeans_r, k=$segm_cond.kmeans_k, method="$segm_cond.kmeans_method") - print(image(skm, key=TRUE, main="K-means clustering", lattice=TRUE, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), contrast.enhance = "$segm_cond.kmeans_imagecontrast", col= colourvector, smooth.image = "$segm_cond.kmeans_imagesmoothing")) + skm = spatialKMeans(msidata, r=$segm_cond.kmeans_r, k=$segm_cond.kmeans_k, method="$segm_cond.kmeans_method") + print(image(skm, key=TRUE, main="K-means clustering", lattice=TRUE, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), contrast.enhance = "$segm_cond.kmeans_imagecontrast", col= colourvector, smooth.image = "$segm_cond.kmeans_imagesmoothing", ylim=c(maximumy+2, 0))) print(plot(skm, main="K-means plot", lattice=TRUE, col= colourvector, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)))) @@ -210,8 +210,8 @@ print('centroids') ##centroids - ssc <- spatialShrunkenCentroids(msidata, r=$segm_cond.centroids_r, k=$segm_cond.centroids_k, s=$segm_cond.centroids_s, method="$segm_cond.centroids_method") - print(image(ssc, key=TRUE, main="Spatial shrunken centroids", lattice=TRUE, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), contrast.enhance = "$segm_cond.centroids_imagecontrast", col= colourvector, smooth.image = "$segm_cond.centroids_imagesmoothing")) + ssc = spatialShrunkenCentroids(msidata, r=$segm_cond.centroids_r, k=$segm_cond.centroids_k, s=$segm_cond.centroids_s, method="$segm_cond.centroids_method") + print(image(ssc, key=TRUE, main="Spatial shrunken centroids", lattice=TRUE, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), contrast.enhance = "$segm_cond.centroids_imagecontrast", col= colourvector, smooth.image = "$segm_cond.centroids_imagesmoothing", ylim=c(maximumy+2, 0))) print(plot(ssc, main="Spatial shrunken centroids plot", lattice=TRUE, col= colourvector, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)))) ssc_classes = (ssc@resultData\$r\$classes) @@ -342,8 +342,8 @@ <param name="feature_color" value="#0000FF"/> </repeat> <output name="segmentationimages" file="pca_imzml.pdf" compare="sim_size" delta="20000"/> - <output name="mzfeatures" file="pcaloadings_results1.txt" compare="sim_size"/> - <output name="pixeloutput" file="pcascores_results1.txt" compare="sim_size"/> + <output name="mzfeatures" file="loadings_pca.tabular" compare="sim_size"/> + <output name="pixeloutput" file="scores_pca.tabular" compare="sim_size"/> </test> <test> <param name="infile" value="" ftype="analyze75"> @@ -362,8 +362,8 @@ <param name="feature_color" value="#00C957"/> </repeat> <output name="segmentationimages" file="kmeans_imzml.pdf" compare="sim_size" delta="20000"/> - <output name="mzfeatures" file="toplabels_results1.txt" compare="sim_size"/> - <output name="pixeloutput" file="cluster_results1.txt" compare="sim_size"/> + <output name="mzfeatures" file="toplabels_skm.tabular" compare="sim_size"/> + <output name="pixeloutput" file="cluster_skm.tabular" compare="sim_size"/> </test> <test> <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/> @@ -384,8 +384,8 @@ <param name="feature_color" value="#848484"/> </repeat> <output name="segmentationimages" file="centroids_imzml.pdf" compare="sim_size" delta="20000"/> - <output name="mzfeatures" file="toplabels_results1.txt" compare="sim_size"/> - <output name="pixeloutput" file="classes_results1.txt" compare="sim_size"/> + <output name="mzfeatures" file="toplabels_ssc.tabular" compare="sim_size"/> + <output name="pixeloutput" file="classes_ssc.tabular" compare="sim_size"/> </test> </tests> <help> |
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| diff -r 0c1a9b68f436 -r d4158c9955ea test-data/centroids_imzml.pdf |
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| Binary file test-data/centroids_imzml.pdf has changed |
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| diff -r 0c1a9b68f436 -r d4158c9955ea test-data/classes_results1.txt --- a/test-data/classes_results1.txt Sat Feb 24 13:51:32 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,10 +0,0 @@ - x -x = 1, y = 1 1 -x = 2, y = 1 1 -x = 3, y = 1 1 -x = 1, y = 2 1 -x = 2, y = 2 1 -x = 3, y = 2 1 -x = 1, y = 3 1 -x = 2, y = 3 1 -x = 3, y = 3 1 |
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| diff -r 0c1a9b68f436 -r d4158c9955ea test-data/classes_ssc.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/classes_ssc.tabular Thu Mar 01 08:26:19 2018 -0500 |
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| @@ -0,0 +1,10 @@ + x +x = 1, y = 1 1 +x = 2, y = 1 1 +x = 3, y = 1 1 +x = 1, y = 2 1 +x = 2, y = 2 1 +x = 3, y = 2 1 +x = 1, y = 3 1 +x = 2, y = 3 1 +x = 3, y = 3 1 |
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| diff -r 0c1a9b68f436 -r d4158c9955ea test-data/cluster_results1.txt --- a/test-data/cluster_results1.txt Sat Feb 24 13:51:32 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,10 +0,0 @@ - x -x = 1, y = 1 3 -x = 2, y = 1 2 -x = 3, y = 1 2 -x = 1, y = 2 2 -x = 2, y = 2 2 -x = 3, y = 2 2 -x = 1, y = 3 1 -x = 2, y = 3 2 -x = 3, y = 3 2 |
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| diff -r 0c1a9b68f436 -r d4158c9955ea test-data/cluster_skm.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster_skm.tabular Thu Mar 01 08:26:19 2018 -0500 |
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| @@ -0,0 +1,10 @@ + x +x = 1, y = 1 3 +x = 2, y = 1 1 +x = 3, y = 1 1 +x = 1, y = 2 1 +x = 2, y = 2 1 +x = 3, y = 2 1 +x = 1, y = 3 2 +x = 2, y = 3 1 +x = 3, y = 3 1 |
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| diff -r 0c1a9b68f436 -r d4158c9955ea test-data/kmeans_imzml.pdf |
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| Binary file test-data/kmeans_imzml.pdf has changed |
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| diff -r 0c1a9b68f436 -r d4158c9955ea test-data/loadings_pca.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/loadings_pca.tabular Thu Mar 01 08:26:19 2018 -0500 |
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| b'@@ -0,0 +1,8400 @@\n+\tPC1\tPC2\n+m/z = 100.08\t-5.85811444155841e-19\t4.67563645911017e-19\n+m/z = 100.17\t-1.59215272704497e-18\t1.29545556462352e-18\n+m/z = 100.25\t1.63451392689733e-18\t-1.31474090407241e-18\n+m/z = 100.33\t2.48270941597418e-19\t-2.14471732080631e-19\n+m/z = 100.42\t2.34894314620814e-18\t-1.90016179215182e-18\n+m/z = 100.5\t-7.45181009466368e-19\t6.10956625723651e-19\n+m/z = 100.58\t-0.000104656106492355\t-0.000353453375099747\n+m/z = 100.67\t-0.00191806412960809\t-0.00647784695026132\n+m/z = 100.75\t-0.00180844223665621\t-0.00610762270489928\n+m/z = 100.83\t0.000360645067163724\t-0.00196796460781247\n+m/z = 100.92\t0.0149012861337974\t-0.00227595239712745\n+m/z = 101\t0.0175435591487301\t0.0143023652391708\n+m/z = 101.08\t0.031002747135816\t-0.0122614203884686\n+m/z = 101.17\t0.0338611449231095\t-0.0223356162474472\n+m/z = 101.25\t0.00673689843629035\t-0.00469328645894402\n+m/z = 101.33\t-6.07248591968161e-06\t7.65206415618374e-07\n+m/z = 101.42\t-8.7285605006811e-09\t-2.94788261457361e-08\n+m/z = 101.5\t3.45834782551742e-07\t1.20261345070282e-06\n+m/z = 101.58\t3.23622451834329e-07\t1.12537180515484e-06\n+m/z = 101.67\t3.86117478477127e-06\t-2.37941054624113e-06\n+m/z = 101.75\t1.16030815032369e-06\t-8.04388710715516e-07\n+m/z = 101.83\t1.00752913826428e-07\t-7.12295619838279e-08\n+m/z = 101.92\t-1.83947514156733e-12\t-6.21243790795034e-12\n+m/z = 102\t-4.17262048378754e-14\t-1.40918758230853e-13\n+m/z = 102.08\t3.30266968225588e-11\t1.1484777208885e-10\n+m/z = 102.17\t2.71286071777003e-10\t-1.38524373101001e-10\n+m/z = 102.25\t1.61761088728649e-10\t-1.07254855324628e-10\n+m/z = 102.33\t2.76943739598385e-11\t-1.9315695760279e-11\n+m/z = 102.42\t-2.89670759294901e-16\t-9.89919504461857e-16\n+m/z = 102.5\t-3.57673851057773e-17\t-1.13137838709792e-16\n+m/z = 102.58\t2.02847312745712e-15\t7.05305368422956e-15\n+m/z = 102.67\t1.45995928099974e-15\t5.08080235002388e-15\n+m/z = 102.75\t1.81355645931963e-14\t-1.13407706336188e-14\n+m/z = 102.83\t4.99451434889525e-15\t-3.46493805095179e-15\n+m/z = 102.92\t3.5590609930103e-16\t-2.53221869805701e-16\n+m/z = 103\t-6.65271632395851e-19\t5.01880339138763e-19\n+m/z = 103.08\t-5.29182193398412e-20\t4.24219607913396e-20\n+m/z = 103.17\t-1.08308254372137e-18\t1.53090778014904e-18\n+m/z = 103.25\t2.0140172965681e-18\t-1.23428494228165e-18\n+m/z = 103.33\t6.5948747628826e-19\t-4.31502445015621e-19\n+m/z = 103.42\t1.15829285209295e-18\t-9.18578323874381e-19\n+m/z = 103.5\t7.64996557530185e-20\t-6.11499914645595e-20\n+m/z = 103.58\t-3.96376219386837e-19\t3.22209858475563e-19\n+m/z = 103.67\t-6.18158027538271e-19\t5.21850678040856e-19\n+m/z = 103.75\t2.51212447788151e-19\t-2.04539641072483e-19\n+m/z = 103.83\t-1.13118208565757e-18\t9.23065173685343e-19\n+m/z = 103.92\t8.59022328826729e-19\t-7.03173001569609e-19\n+m/z = 104\t6.42791081949006e-20\t-5.09471219107003e-20\n+m/z = 104.08\t-7.73702193533547e-19\t6.35560525449952e-19\n+m/z = 104.17\t4.17934916777221e-19\t-3.36591203136874e-19\n+m/z = 104.25\t-8.01082847078073e-19\t6.33870455154861e-19\n+m/z = 104.33\t1.31679769529789e-18\t-1.09457644857517e-18\n+m/z = 104.42\t8.53652984445634e-19\t-7.09046174103633e-19\n+m/z = 104.5\t-1.32729897350366e-18\t1.06101657501984e-18\n+m/z = 104.58\t-1.10949121723327e-18\t8.86382197332373e-19\n+m/z = 104.67\t-1.26009825490333e-18\t1.01767561272778e-18\n+m/z = 104.75\t1.00700454926584e-18\t-7.99676621006995e-19\n+m/z = 104.83\t2.63226402912176e-19\t-2.0886467463537e-19\n+m/z = 104.92\t7.28099510855941e-19\t-5.89019122279884e-19\n+m/z = 105\t-1.16136322796224e-18\t9.33375216908331e-19\n+m/z = 105.08\t1.4329085782091e-19\t-1.11920860620786e-19\n+m/z = 105.17\t-6.04272845469955e-19\t4.88221747854317e-19\n+m/z = 105.25\t-1.55764714886487e-18\t1.25482364948323e-18\n+m/z = 105.33\t2.28470713117219e-18\t-1.8431367473114e-18\n+m/z = 105.42\t4.24073781198572e-19\t-3.43761034406124e-19\n+m/z = 105.5\t3.14983624201331e-19\t-2.53533350409124e-19\n+m/z = 105.58\t-6.52620969795775e-19\t5.32146736817344e-19\n+m/z = 105.67\t4.2548701251123e-19\t-3.45126802720901e-19\n+m/z = 105.75\t1.03961531671925e-18\t-8.37212825377058e-19\n+m/z = 105.83\t5.66167234663928e-19\t-4.43164714765139e-19\n+m/z = 105.92\t-1.00890864404629e'..b'958861291e-07\t4.09983128264202e-07\n+m/z = 794.08\t-1.02067038585584e-07\t1.45258975023008e-07\n+m/z = 794.17\t-1.12379272171344e-08\t1.59935059499399e-08\n+m/z = 794.25\t3.39762648316736e-19\t-2.75760988449864e-19\n+m/z = 794.33\t1.93113279467806e-18\t-1.5699335842303e-18\n+m/z = 794.42\t-3.76940058489683e-19\t3.06246311803983e-19\n+m/z = 794.5\t1.46563646585253e-18\t-1.19335634087156e-18\n+m/z = 794.58\t-0.004775416800786\t0.00754050838457728\n+m/z = 794.67\t0.0045727839869588\t0.0426132474217616\n+m/z = 794.75\t0.00833966396316629\t0.0346155215563305\n+m/z = 794.83\t0.00096664475481058\t0.00353481494848328\n+m/z = 794.92\t-0.00195096214440754\t-0.00658284942421866\n+m/z = 795\t-0.000640470913415032\t-0.00216305205292817\n+m/z = 795.08\t-5.9941006222702e-05\t-0.000202437790458378\n+m/z = 795.17\t-5.40140143892465e-07\t7.68712453674048e-07\n+m/z = 795.25\t7.01767360339006e-07\t3.35591597300876e-06\n+m/z = 795.33\t3.18791439544673e-07\t1.20612425912601e-06\n+m/z = 795.42\t-8.91159484698589e-08\t-2.9688619162874e-07\n+m/z = 795.5\t-8.73188753124494e-08\t-2.94900624757929e-07\n+m/z = 795.58\t-1.56512048749326e-08\t-5.28585609794844e-08\n+m/z = 795.67\t-3.01232756767804e-11\t4.28706085816637e-11\n+m/z = 795.75\t1.48510034969993e-11\t1.72677972199933e-10\n+m/z = 795.83\t3.85060929918801e-11\t1.57275897335223e-10\n+m/z = 795.92\t9.04270409935284e-12\t3.14452965232502e-11\n+m/z = 796\t-9.44016066061441e-12\t-3.18744897876405e-11\n+m/z = 796.08\t-2.76488434003364e-12\t-9.33779830821354e-12\n+m/z = 796.17\t-2.1572379784191e-13\t-7.28563309485137e-13\n+m/z = 796.25\t-2.58428538869161e-15\t3.67659962489166e-15\n+m/z = 796.33\t3.49532597970038e-15\t1.61264176994389e-14\n+m/z = 796.42\t1.40475919945419e-15\t5.24762147924244e-15\n+m/z = 796.5\t-5.44876161259713e-16\t-1.81635204033388e-15\n+m/z = 796.58\t-3.91578379074872e-16\t-1.3187636258036e-15\n+m/z = 796.67\t-0.0111966558774575\t0.00184642752951265\n+m/z = 796.75\t-0.00616492950080406\t0.00101665137094269\n+m/z = 796.83\t-0.000947322559573781\t0.000156221864141353\n+m/z = 796.92\t1.19347891860796e-18\t-1.58186315550908e-19\n+m/z = 797\t6.40224622505014e-19\t-3.63013800235767e-19\n+m/z = 797.08\t9.86570157920768e-20\t-2.67279572231496e-19\n+m/z = 797.17\t-6.18529780130968e-08\t1.02001028377594e-08\n+m/z = 797.25\t-7.22222614326424e-07\t1.19100893349061e-07\n+m/z = 797.33\t-1.81894222729473e-07\t2.99959652218137e-08\n+m/z = 797.42\t-9.21039873864868e-09\t1.51887617046508e-09\n+m/z = 797.5\t-1.35867181729443e-18\t1.06025084932238e-18\n+m/z = 797.58\t-5.78838679388108e-19\t4.71470730313539e-19\n+m/z = 797.67\t2.98627668731271e-19\t-2.42842948573192e-19\n+m/z = 797.75\t-6.1964596211569e-11\t1.02185093896369e-11\n+m/z = 797.83\t-2.72928150819404e-11\t4.50082668752482e-12\n+m/z = 797.92\t-0.00389097733292416\t0.00553753088718718\n+m/z = 798\t-0.00407514724498001\t0.00579963639658722\n+m/z = 798.08\t-0.000963732393772134\t0.00137155718100154\n+m/z = 798.17\t-3.59243592475196e-05\t5.11265505001427e-05\n+m/z = 798.25\t-1.5842306784995e-15\t2.60975838521843e-16\n+m/z = 798.33\t-3.32803643538276e-15\t5.48984436966452e-16\n+m/z = 798.42\t-7.70174299676523e-16\t1.26614168799509e-16\n+m/z = 798.5\t-3.69626374553333e-07\t5.26041992105245e-07\n+m/z = 798.58\t5.18525840962844e-05\t0.00040742972209897\n+m/z = 798.67\t0.00374645335939338\t0.0293383545235387\n+m/z = 798.75\t0.00291920523455569\t0.0228600645485006\n+m/z = 798.83\t0.000533036946002713\t0.00417417002686771\n+m/z = 798.92\t-3.33828988788543e-19\t1.94609669840873e-19\n+m/z = 799\t-1.39504213617174e-11\t1.98538518657542e-11\n+m/z = 799.08\t-1.86620420858138e-11\t2.65593000640013e-11\n+m/z = 799.17\t-4.06033466667059e-12\t5.77855646801887e-12\n+m/z = 799.25\t3.15016300887051e-07\t2.46686834032219e-06\n+m/z = 799.33\t9.32606479033912e-08\t7.30316733348658e-07\n+m/z = 799.42\t7.58575172172955e-09\t5.94034197783443e-08\n+m/z = 799.5\t-4.87638510402758e-20\t3.93441017682795e-20\n+m/z = 799.58\t0.000152206860922684\t0.00119191985005999\n+m/z = 799.67\t0.001748531535768\t0.0136926117080106\n+m/z = 799.75\t0.00121053975241952\t0.00947964074305659\n+m/z = 799.83\t0.000239952374183472\t0.0018790480016507\n+m/z = 799.92\t-1.09747302731703e-19\t8.8028372827583e-20\n' |
| b |
| diff -r 0c1a9b68f436 -r d4158c9955ea test-data/pca_imzml.pdf |
| b |
| Binary file test-data/pca_imzml.pdf has changed |
| b |
| diff -r 0c1a9b68f436 -r d4158c9955ea test-data/pcaloadings_results1.txt --- a/test-data/pcaloadings_results1.txt Sat Feb 24 13:51:32 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,8400 +0,0 @@\n-\tPC1\tPC2\n-m/z = 100.08\t-1.86059990031193e-19\t-4.20095088814001e-19\n-m/z = 100.17\t9.87509444691618e-20\t2.35147879854537e-19\n-m/z = 100.25\t1.09097027695743e-19\t2.4228535983709e-19\n-m/z = 100.33\t-2.08830496743711e-20\t-4.85115687658163e-20\n-m/z = 100.42\t3.15093935579793e-19\t7.61345646065437e-19\n-m/z = 100.5\t4.73643315429366e-20\t1.16213766542198e-19\n-m/z = 100.58\t-0.000104656106492356\t0.000353453375099747\n-m/z = 100.67\t-0.00191806412960808\t0.00647784695026133\n-m/z = 100.75\t-0.00180844223665621\t0.00610762270489929\n-m/z = 100.83\t0.000360645067163725\t0.00196796460781247\n-m/z = 100.92\t0.0149012861337974\t0.00227595239712752\n-m/z = 101\t0.0175435591487301\t-0.0143023652391706\n-m/z = 101.08\t0.031002747135816\t0.0122614203884688\n-m/z = 101.17\t0.0338611449231094\t0.0223356162474473\n-m/z = 101.25\t0.00673689843629034\t0.00469328645894403\n-m/z = 101.33\t-6.07248591968159e-06\t-7.65206415618305e-07\n-m/z = 101.42\t-8.72856050015876e-09\t2.94788261457765e-08\n-m/z = 101.5\t3.45834782552111e-07\t-1.20261345070239e-06\n-m/z = 101.58\t3.23622451834405e-07\t-1.12537180515533e-06\n-m/z = 101.67\t3.8611747847706e-06\t2.37941054624083e-06\n-m/z = 101.75\t1.16030815032252e-06\t8.0438871071427e-07\n-m/z = 101.83\t1.00752913826984e-07\t7.12295619845451e-08\n-m/z = 101.92\t-1.83947711227944e-12\t6.21243627026478e-12\n-m/z = 102\t-4.17258893310736e-14\t1.40918554344855e-13\n-m/z = 102.08\t3.30267002709013e-11\t-1.14847768724187e-10\n-m/z = 102.17\t2.71286069592646e-10\t1.38524371581216e-10\n-m/z = 102.25\t1.61761087755614e-10\t1.07254853863827e-10\n-m/z = 102.33\t2.76943739547824e-11\t1.93156959489091e-11\n-m/z = 102.42\t-2.92749887941464e-16\t9.86940330694681e-16\n-m/z = 102.5\t-3.4051403301236e-17\t1.14403988503004e-16\n-m/z = 102.58\t2.02823230444141e-15\t-7.05332921030856e-15\n-m/z = 102.67\t1.46068550491091e-15\t-5.08048086214669e-15\n-m/z = 102.75\t1.81356277671187e-14\t1.13406889067328e-14\n-m/z = 102.83\t4.99459890522449e-15\t3.46465652724235e-15\n-m/z = 102.92\t3.54654620472745e-16\t2.52101917234947e-16\n-m/z = 103\t-7.33633722360385e-20\t-1.20274920856386e-19\n-m/z = 103.08\t1.41618326920922e-19\t3.72875524743884e-19\n-m/z = 103.17\t-2.19975190398912e-19\t-1.43359941267792e-18\n-m/z = 103.25\t1.42891908175342e-18\t7.88710114358005e-19\n-m/z = 103.33\t6.41297597138591e-19\t2.78255342751776e-19\n-m/z = 103.42\t8.46894101356055e-20\t1.65833163524832e-20\n-m/z = 103.5\t-1.50221528863782e-19\t-3.58744763503543e-19\n-m/z = 103.58\t-1.82850015700516e-19\t-4.2644833675042e-19\n-m/z = 103.67\t-1.84122111338174e-19\t-4.38571120486911e-19\n-m/z = 103.75\t-9.30780295318121e-21\t-2.3520100648106e-20\n-m/z = 103.83\t-1.65598948043249e-19\t-4.22198345569072e-19\n-m/z = 103.92\t-6.85264194378445e-20\t-1.6350267764531e-19\n-m/z = 104\t2.54015057897185e-19\t6.10979475376383e-19\n-m/z = 104.08\t-2.73920283032827e-20\t-6.21437335507252e-20\n-m/z = 104.17\t-2.58053385535497e-19\t-6.04029115522955e-19\n-m/z = 104.25\t4.75925321388198e-20\t1.09512432077898e-19\n-m/z = 104.33\t-3.75580297011702e-20\t-8.36745295564117e-20\n-m/z = 104.42\t-2.12364245926505e-19\t-4.94251798114715e-19\n-m/z = 104.5\t-5.31202059801377e-20\t-1.25121350810266e-19\n-m/z = 104.58\t2.22992656193459e-19\t5.07814577079916e-19\n-m/z = 104.67\t1.54152506561108e-19\t3.75142976244701e-19\n-m/z = 104.75\t4.89928677667099e-22\t1.22217765622567e-21\n-m/z = 104.83\t-8.33910883636569e-20\t-1.87553590799543e-19\n-m/z = 104.92\t3.97572052143163e-19\t9.09541583209455e-19\n-m/z = 105\t-1.60052339088906e-20\t-3.72476803115141e-20\n-m/z = 105.08\t-5.78938586011886e-19\t-1.244036263573e-18\n-m/z = 105.17\t2.30372523518939e-19\t5.47162607642138e-19\n-m/z = 105.25\t-1.1729116805124e-19\t-2.74476091908414e-19\n-m/z = 105.33\t2.7177988163347e-19\t6.01578056987235e-19\n-m/z = 105.42\t-2.81678455627353e-19\t-5.89635523196556e-19\n-m/z = 105.5\t1.1333783354223e-19\t2.35283579480262e-19\n-m/z = 105.58\t-2.73342047052725e-19\t-6.47903025224876e-19\n-m/z = 105.67\t-2.51516708177392e-19\t-6.02295018812391e-19\n-m/z = 105.75\t1.50419796039407e-19\t3.46882189159088e-19\n-m/z = 105.83\t3.12785438881079e-19\t7.77753325844277e-19\n-m/z = 105.92\t-4.27089286960678e-19\t-1.0002810'..b'\n-m/z = 794.08\t-1.02067038586458e-07\t-1.45258975024606e-07\n-m/z = 794.17\t-1.12379272165959e-08\t-1.59935059494185e-08\n-m/z = 794.25\t-1.79445928966385e-19\t-4.00703216842676e-19\n-m/z = 794.33\t1.76267271134409e-19\t4.56914921805518e-19\n-m/z = 794.42\t2.17003145239192e-19\t5.24137377545813e-19\n-m/z = 794.5\t-4.21250006381354e-20\t-9.94030493712647e-20\n-m/z = 794.58\t-0.00477541680078601\t-0.00754050838457741\n-m/z = 794.67\t0.00457278398695885\t-0.0426132474217616\n-m/z = 794.75\t0.00833966396316635\t-0.0346155215563303\n-m/z = 794.83\t0.000966644754810597\t-0.00353481494848323\n-m/z = 794.92\t-0.00195096214440753\t0.00658284942421867\n-m/z = 795\t-0.000640470913415029\t0.00216305205292817\n-m/z = 795.08\t-5.99410062227027e-05\t0.000202437790458378\n-m/z = 795.17\t-5.4014014389065e-07\t-7.68712453672831e-07\n-m/z = 795.25\t7.01767360337984e-07\t-3.35591597300961e-06\n-m/z = 795.33\t3.18791439545021e-07\t-1.2061242591259e-06\n-m/z = 795.42\t-8.91159484677643e-08\t2.9688619163037e-07\n-m/z = 795.5\t-8.7318875313056e-08\t2.94900624757305e-07\n-m/z = 795.58\t-1.56512048740352e-08\t5.28585609798675e-08\n-m/z = 795.67\t-3.01232741113653e-11\t-4.28706071552815e-11\n-m/z = 795.75\t1.48510028562637e-11\t-1.72677973322058e-10\n-m/z = 795.83\t3.8506092534405e-11\t-1.57275897191402e-10\n-m/z = 795.92\t9.04270346863403e-12\t-3.1445297664552e-11\n-m/z = 796\t-9.44016302806483e-12\t3.187448742336e-11\n-m/z = 796.08\t-2.76488416961386e-12\t9.33779840109984e-12\n-m/z = 796.17\t-2.15724645944791e-13\t7.28562321344289e-13\n-m/z = 796.25\t-2.58221231300034e-15\t-3.67492240117948e-15\n-m/z = 796.33\t3.49525520050498e-15\t-1.61257132943202e-14\n-m/z = 796.42\t1.40468494659126e-15\t-5.24764603502545e-15\n-m/z = 796.5\t-5.43139987078557e-16\t1.81732754308213e-15\n-m/z = 796.58\t-3.90875838968025e-16\t1.31905830414735e-15\n-m/z = 796.67\t-0.0111966558774574\t-0.00184642752951266\n-m/z = 796.75\t-0.00616492950080404\t-0.0010166513709427\n-m/z = 796.83\t-0.000947322559573778\t-0.000156221864141355\n-m/z = 796.92\t4.11662469614298e-19\t-1.3216270704391e-19\n-m/z = 797\t-2.17759482515273e-19\t-7.43488309644877e-19\n-m/z = 797.08\t1.79350141189194e-19\t7.44535109941237e-19\n-m/z = 797.17\t-6.18529780126893e-08\t-1.0200102837658e-08\n-m/z = 797.25\t-7.22222614326598e-07\t-1.19100893349065e-07\n-m/z = 797.33\t-1.818942227306e-07\t-2.99959652232607e-08\n-m/z = 797.42\t-9.21039873681872e-09\t-1.51887616891841e-09\n-m/z = 797.5\t6.69667341120041e-20\t1.59012431693488e-19\n-m/z = 797.58\t1.66103283550513e-19\t3.93901432945403e-19\n-m/z = 797.67\t-1.36211415086825e-19\t-2.97929530446326e-19\n-m/z = 797.75\t-6.19645961970517e-11\t-1.02185086744297e-11\n-m/z = 797.83\t-2.72928150794626e-11\t-4.50082713427092e-12\n-m/z = 797.92\t-0.00389097733292416\t-0.00553753088718729\n-m/z = 798\t-0.00407514724498002\t-0.00579963639658733\n-m/z = 798.08\t-0.000963732393772135\t-0.00137155718100157\n-m/z = 798.17\t-3.59243592475192e-05\t-5.11265505001433e-05\n-m/z = 798.25\t-1.58505824753274e-15\t-2.62341211169423e-16\n-m/z = 798.33\t-3.32795606248157e-15\t-5.4914371746535e-16\n-m/z = 798.42\t-7.70622667488165e-16\t-1.2671683736167e-16\n-m/z = 798.5\t-3.69626374554309e-07\t-5.26041992105907e-07\n-m/z = 798.58\t5.18525840962871e-05\t-0.000407429722098979\n-m/z = 798.67\t0.0037464533593935\t-0.0293383545235394\n-m/z = 798.75\t0.00291920523455579\t-0.0228600645485012\n-m/z = 798.83\t0.000533036946002732\t-0.00417417002686781\n-m/z = 798.92\t-2.12094854281441e-19\t-2.42407615253506e-19\n-m/z = 799\t-1.39504211917673e-11\t-1.98538524645768e-11\n-m/z = 799.08\t-1.8662042267273e-11\t-2.65593005367568e-11\n-m/z = 799.17\t-4.06033618452523e-12\t-5.77855774543026e-12\n-m/z = 799.25\t3.15016300887783e-07\t-2.46686834032146e-06\n-m/z = 799.33\t9.32606479023616e-08\t-7.30316733349191e-07\n-m/z = 799.42\t7.58575172019168e-09\t-5.94034197795049e-08\n-m/z = 799.5\t6.19356981829876e-20\t1.45261958914268e-19\n-m/z = 799.58\t0.000152206860922688\t-0.00119191985006002\n-m/z = 799.67\t0.00174853153576805\t-0.0136926117080109\n-m/z = 799.75\t0.00121053975241956\t-0.00947964074305681\n-m/z = 799.83\t0.00023995237418348\t-0.00187904800165075\n-m/z = 799.92\t-1.61416057845098e-19\t-3.77958420663974e-19\n' |
| b |
| diff -r 0c1a9b68f436 -r d4158c9955ea test-data/pcascores_results1.txt --- a/test-data/pcascores_results1.txt Sat Feb 24 13:51:32 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,10 +0,0 @@ - PC1 PC2 -x = 1, y = 1 -3.10354953946922 0.882256622295169 -x = 2, y = 1 0.896503112130733 -2.98575442188371 -x = 3, y = 1 -1.57899570254884 2.26797345312228 -x = 1, y = 2 4.34938743071701 -6.43242810521544 -x = 2, y = 2 -4.25927282262866 -0.298723132409794 -x = 3, y = 2 -3.62418135901873 0.627868439327948 -x = 1, y = 3 -3.27840077885159 -1.9843074587809 -x = 2, y = 3 -1.38097137864788 4.74863282848963 -x = 3, y = 3 11.9794810383172 3.17448177505485 |
| b |
| diff -r 0c1a9b68f436 -r d4158c9955ea test-data/scores_pca.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scores_pca.tabular Thu Mar 01 08:26:19 2018 -0500 |
| b |
| @@ -0,0 +1,10 @@ + PC1 PC2 +x = 1, y = 1 -3.10354953946921 -0.882256622295146 +x = 2, y = 1 0.896503112130722 2.98575442188366 +x = 3, y = 1 -1.57899570254884 -2.26797345312228 +x = 1, y = 2 4.349387430717 6.43242810521547 +x = 2, y = 2 -4.25927282262867 0.298723132409784 +x = 3, y = 2 -3.62418135901872 -0.62786843932794 +x = 1, y = 3 -3.27840077885159 1.98430745878087 +x = 2, y = 3 -1.38097137864787 -4.74863282848963 +x = 3, y = 3 11.9794810383172 -3.17448177505483 |
| b |
| diff -r 0c1a9b68f436 -r d4158c9955ea test-data/toplabels_results1.txt --- a/test-data/toplabels_results1.txt Sat Feb 24 13:51:32 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,501 +0,0 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|
| b |
| diff -r 0c1a9b68f436 -r d4158c9955ea test-data/toplabels_skm.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/toplabels_skm.tabular Thu Mar 01 08:26:19 2018 -0500 |
| b |
| b'@@ -0,0 +1,501 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|
| b |
| diff -r 0c1a9b68f436 -r d4158c9955ea test-data/toplabels_ssc.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/toplabels_ssc.tabular Thu Mar 01 08:26:19 2018 -0500 |
| b |
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