| Previous changeset 7:adfef12c7e31 (2018-07-06) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 |
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modified:
segmentation_tool.xml test-data/centroids_rdata.pdf test-data/classes_ssc.tabular test-data/cluster_skm.RData test-data/cluster_skm.tabular test-data/kmeans_analyze.pdf test-data/loadings_pca.tabular test-data/pca_imzml.pdf test-data/scores_pca.tabular test-data/toplabels_skm.tabular test-data/toplabels_ssc.tabular |
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| diff -r adfef12c7e31 -r 4a62874c21a3 segmentation_tool.xml --- a/segmentation_tool.xml Fri Jul 06 14:14:27 2018 -0400 +++ b/segmentation_tool.xml Wed Aug 22 13:44:28 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="mass_spectrometry_imaging_segmentations" name="MSI segmentation" version="1.10.0.3"> +<tool id="mass_spectrometry_imaging_segmentations" name="MSI segmentation" version="1.10.0.4"> <description>mass spectrometry imaging spatial clustering</description> <requirements> <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> @@ -45,7 +45,11 @@ #elif $infile.ext == 'analyze75' msidata = readAnalyze('infile') #else - load('infile.RData') + loadRData <- function(fileName){ + load(fileName) + get(ls()[ls() != "fileName"]) + } + msidata = loadRData('infile.RData') #end if @@ -186,6 +190,8 @@ #end if + ## set seed to make analysis reproducible + set.seed($setseed) #if str( $segm_cond.segmentationtool ) == 'pca': print('pca') @@ -198,9 +204,9 @@ method = "$segm_cond.pca_method", scale = $segm_cond.pca_scale, layout = c(ncomp, 1)) ### images in pdf file - print(image(pca_result, main="PCA image", lattice=lattice_input, strip = strip_input, col=colourvector)) + print(image(pca_result, main="PCA image", lattice=lattice_input, strip = strip_input, col=colourvector, ylim=c(maximumy+2, minimumy-2))) for (PCs in 1:$segm_cond.pca_ncomp){ - print(image(pca_result, column = c(paste0("PC",PCs)), lattice=lattice_input, superpose = FALSE, col.regions = risk.colors(100)))} + print(image(pca_result, column = c(paste0("PC",PCs)), lattice=lattice_input, superpose = FALSE, col.regions = risk.colors(100), ylim=c(maximumy+2, minimumy-2)))} ### plots in pdf file print(plot(pca_result, main="PCA plot", lattice=lattice_input, col= colourvector, strip = strip_input)) for (PCs in 1:$segm_cond.pca_ncomp){ @@ -208,10 +214,14 @@ ### values in tabular files pcaloadings = (pca_result@resultData\$ncomp\$loadings) ### loading for each m/z value + pcaloadings2 = cbind(rownames(pcaloadings), pcaloadings) + colnames(pcaloadings2) = c("mz", colnames(pcaloadings)) pcascores = (pca_result@resultData\$ncomp\$scores) ### scores for each pixel + pcascores2 = cbind(rownames(pcascores), pcascores) + colnames(pcascores2) = c("pixel names", colnames(pcascores)) - write.table(pcaloadings, file="$mzfeatures", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t") - write.table(pcascores, file="$pixeloutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t") + write.table(pcaloadings2, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") + write.table(pcascores2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") ## optional output as .RData #if $output_rdata: @@ -225,7 +235,7 @@ ##k-means skm = spatialKMeans(msidata, r=c($segm_cond.kmeans_r), k=c($segm_cond.kmeans_k), method="$segm_cond.kmeans_method") - print(image(skm, key=TRUE, main="K-means clustering", lattice=lattice_input, strip=strip_input, col= colourvector, layout=c(1,1))) + 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($segm_cond.kmeans_layout))) @@ -233,12 +243,13 @@ for (iteration in 1:length(skm@resultData)){ skm_cluster = ((skm@resultData)[[iteration]]\$cluster) skm_clusters = cbind(skm_clusters, skm_cluster) } - colnames(skm_clusters) = names((skm@resultData)) + skm_clusters2 = cbind(rownames(skm_clusters), skm_clusters) + colnames(skm_clusters2) = c("pixel names", names(skm@resultData)) skm_toplabels = topLabels(skm, n=$segm_cond.kmeans_toplabels) - - write.table(skm_toplabels, file="$mzfeatures", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t") - write.table(skm_clusters, file="$pixeloutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t") + + write.table(skm_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") + write.table(skm_clusters2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") ## optional output as .RData #if $output_rdata: @@ -253,7 +264,7 @@ ##centroids ssc = spatialShrunkenCentroids(msidata, r=c($segm_cond.centroids_r), k=c($segm_cond.centroids_k), s=c($segm_cond.centroids_s), method="$segm_cond.centroids_method") - print(image(ssc, key=TRUE, main="Spatial shrunken centroids", lattice=lattice_input, strip = strip_input, col= colourvector,layout=c(1,1))) + print(image(ssc, key=TRUE, main="Spatial shrunken centroids", lattice=lattice_input, strip = strip_input, col= colourvector,layout=c(1,1), ylim=c(maximumy+2, minimumy-2))) print(plot(ssc, main="Spatial shrunken centroids plot", lattice=lattice_input, col= colourvector, strip = strip_input,layout=c($segm_cond.centroids_layout))) print(plot(ssc, mode = "tstatistics",key = TRUE, lattice=lattice_input, layout = c($segm_cond.centroids_layout), main="t-statistics", col=colourvector)) plot(summary(ssc), main = "Number of segments") @@ -262,12 +273,13 @@ for (iteration in 1:length(ssc@resultData)){ ssc_class = ((ssc@resultData)[[iteration]]\$classes) ssc_classes = cbind(ssc_classes, ssc_class) } - colnames(ssc_classes) = names((ssc@resultData)) + ssc_classes2 = cbind(rownames(ssc_classes), ssc_classes) + colnames(ssc_classes2) = c("pixel names", names(ssc@resultData)) ssc_toplabels = topLabels(ssc, n=$segm_cond.centroids_toplabels) - write.table(ssc_toplabels, file="$mzfeatures", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t") - write.table(ssc_classes, file="$pixeloutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t") + write.table(ssc_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") + write.table(ssc_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") ## optional output as .RData #if $output_rdata: @@ -379,6 +391,7 @@ </param> </repeat> <param name="output_rdata" type="boolean" display="radio" label="Results as .RData output"/> + <param name="setseed" type="integer" value="1" label="set seed" help="use same value to reproduce previous results"/> </inputs> <outputs> <data format="pdf" name="segmentationimages" from_work_dir="segmentationpdf.pdf" label = "$infile.display_name segmentation"/> |
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| diff -r adfef12c7e31 -r 4a62874c21a3 test-data/centroids_rdata.pdf |
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| Binary file test-data/centroids_rdata.pdf has changed |
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| diff -r adfef12c7e31 -r 4a62874c21a3 test-data/classes_ssc.tabular --- a/test-data/classes_ssc.tabular Fri Jul 06 14:14:27 2018 -0400 +++ b/test-data/classes_ssc.tabular Wed Aug 22 13:44:28 2018 -0400 |
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| @@ -1,4 +1,4 @@ - r = 1, k = 3, s = 2 r = 2, k = 3, s = 2 +pixel names r = 1, k = 3, s = 2 r = 2, k = 3, s = 2 x = 1, y = 1 1 1 x = 2, y = 1 2 2 x = 3, y = 1 2 2 |
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| diff -r adfef12c7e31 -r 4a62874c21a3 test-data/cluster_skm.RData |
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| Binary file test-data/cluster_skm.RData has changed |
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| diff -r adfef12c7e31 -r 4a62874c21a3 test-data/cluster_skm.tabular --- a/test-data/cluster_skm.tabular Fri Jul 06 14:14:27 2018 -0400 +++ b/test-data/cluster_skm.tabular Wed Aug 22 13:44:28 2018 -0400 |
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| @@ -1,10 +1,10 @@ - r = 1, k = 2 r = 1, k = 3 r = 2, k = 2 r = 2, k = 3 r = 3, k = 2 r = 3, k = 3 -x = 1, y = 1 1 3 1 3 1 1 +pixel names r = 1, k = 2 r = 1, k = 3 r = 2, k = 2 r = 2, k = 3 r = 3, k = 2 r = 3, k = 3 +x = 1, y = 1 1 1 1 1 1 3 x = 2, y = 1 2 2 2 2 2 2 -x = 3, y = 1 2 1 1 1 1 1 -x = 1, y = 2 1 3 1 3 1 1 +x = 3, y = 1 2 3 1 3 1 3 +x = 1, y = 2 1 1 1 1 1 3 x = 2, y = 2 2 2 2 2 2 2 -x = 3, y = 2 2 1 1 1 1 1 -x = 1, y = 3 1 3 1 3 1 3 +x = 3, y = 2 2 3 1 3 1 3 +x = 1, y = 3 1 1 1 1 1 1 x = 2, y = 3 2 2 2 2 2 2 -x = 3, y = 3 2 1 1 1 1 1 +x = 3, y = 3 2 3 1 3 1 3 |
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| diff -r adfef12c7e31 -r 4a62874c21a3 test-data/kmeans_analyze.pdf |
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| Binary file test-data/kmeans_analyze.pdf has changed |
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| diff -r adfef12c7e31 -r 4a62874c21a3 test-data/loadings_pca.tabular --- a/test-data/loadings_pca.tabular Fri Jul 06 14:14:27 2018 -0400 +++ b/test-data/loadings_pca.tabular Wed Aug 22 13:44:28 2018 -0400 |
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| b'@@ -1,1200 +1,1200 @@\n-\tPC1\tPC2\n-m/z = 300.08\t-0.00431122859758326\t0.00526403166713945\n-m/z = 300.17\t-0.000423445750267206\t0.000517029377651584\n-m/z = 300.25\t4.65194104914721e-11\t-4.22150066716968e-11\n-m/z = 300.33\t1.35108622449329e-11\t-1.22607141402685e-11\n-m/z = 300.42\t1.05327875556794e-12\t-9.55818546824256e-13\n-m/z = 300.5\t-8.10333136004702e-07\t9.89420809475108e-07\n-m/z = 300.58\t-5.81387112969683e-07\t7.09876570969675e-07\n-m/z = 300.67\t-1.0703278978058e-07\t1.30687571317884e-07\n-m/z = 300.75\t3.42214918580322e-15\t-3.09915337255164e-15\n-m/z = 300.83\t1.90764072894432e-15\t-1.73329226842089e-15\n-m/z = 300.92\t3.12142851038551e-16\t-2.83527661692011e-16\n-m/z = 301\t1.3656585759233e-18\t5.31264736682766e-19\n-m/z = 301.08\t-6.24592344872316e-11\t7.62630431761411e-11\n-m/z = 301.17\t-1.86468427378312e-11\t2.27678906993735e-11\n-m/z = 301.25\t-1.54395078943368e-12\t1.88517048352715e-12\n-m/z = 301.33\t-3.12052218099988e-19\t-3.97244373430137e-19\n-m/z = 301.42\t-1.89903704823836e-19\t-1.57169759096181e-19\n-m/z = 301.5\t-8.03843231302489e-19\t-3.83583084342369e-19\n-m/z = 301.58\t-4.42691457076648e-15\t5.40639048800054e-15\n-m/z = 301.67\t-2.61009660754888e-15\t3.18104997229853e-15\n-m/z = 301.75\t-4.38426969699555e-16\t5.35743419967843e-16\n-m/z = 301.83\t1.36542935950992e-18\t5.36493896249926e-19\n-m/z = 301.92\t-4.03711932656413e-18\t-1.66919171399678e-18\n-m/z = 302\t-1.61042996275192e-18\t-8.21783337412095e-19\n-m/z = 302.08\t-1.06750116645735e-18\t-4.71631528565016e-19\n-m/z = 302.17\t1.35819163216585e-18\t1.06960551236743e-18\n-m/z = 302.25\t3.69334636239439e-19\t2.75094282188811e-19\n-m/z = 302.33\t6.16238677010334e-19\t2.59719561769406e-19\n-m/z = 302.42\t-9.87994863569276e-19\t-4.56126853547735e-19\n-m/z = 302.5\t2.11856781850494e-18\t8.8461919176002e-19\n-m/z = 302.58\t-2.03979793603573e-18\t-8.7588636572893e-19\n-m/z = 302.67\t0.00238735543431954\t0.000597177601535268\n-m/z = 302.75\t0.0422753281275894\t0.0105748304975568\n-m/z = 302.83\t0.0478251463644704\t0.0119630725230271\n-m/z = 302.92\t0.0117873138328592\t0.00294850096557017\n+mz\tPC1\tPC2\n+m/z = 300.08\t-0.00431122859758329\t0.00526403166713949\n+m/z = 300.17\t-0.000423445750267208\t0.00051702937765159\n+m/z = 300.25\t4.65194150536899e-11\t-4.22150087099464e-11\n+m/z = 300.33\t1.35108612188122e-11\t-1.22607072500498e-11\n+m/z = 300.42\t1.05327734584566e-12\t-9.55817595104931e-13\n+m/z = 300.5\t-8.10333136001904e-07\t9.89420809472527e-07\n+m/z = 300.58\t-5.81387112967612e-07\t7.09876570972713e-07\n+m/z = 300.67\t-1.07032789780076e-07\t1.3068757132126e-07\n+m/z = 300.75\t3.41674858316537e-15\t-3.099477097213e-15\n+m/z = 300.83\t1.91005306978273e-15\t-1.73400711936836e-15\n+m/z = 300.92\t3.0935599995382e-16\t-2.77380998949046e-16\n+m/z = 301\t-6.65648097524728e-19\t1.46948889144108e-18\n+m/z = 301.08\t-6.24592367703673e-11\t7.62630392533733e-11\n+m/z = 301.17\t-1.86468400473725e-11\t2.27678809866643e-11\n+m/z = 301.25\t-1.54395235623673e-12\t1.88517524320557e-12\n+m/z = 301.33\t2.98688326385702e-19\t-3.5847546239491e-19\n+m/z = 301.42\t8.89316552145388e-20\t-1.13353541808862e-19\n+m/z = 301.5\t-1.80421834428211e-18\t3.57218991846548e-18\n+m/z = 301.58\t-4.42908079426941e-15\t5.40912624674897e-15\n+m/z = 301.67\t-2.60749760943137e-15\t3.18475128356288e-15\n+m/z = 301.75\t-4.40359280065527e-16\t5.39122160392572e-16\n+m/z = 301.83\t-1.38008713975051e-18\t2.88001159253086e-18\n+m/z = 301.92\t-1.40307577498072e-19\t2.77975673360276e-19\n+m/z = 302\t3.62667249262872e-18\t-7.13083020490704e-18\n+m/z = 302.08\t-1.08392092461489e-18\t2.3266850449903e-18\n+m/z = 302.17\t-1.89685413709983e-19\t1.23861281753609e-19\n+m/z = 302.25\t1.84071706842555e-19\t-4.72845441155538e-19\n+m/z = 302.33\t2.65842917715123e-18\t-5.67839989734713e-18\n+m/z = 302.42\t8.89384394284211e-19\t-1.78363962868074e-18\n+m/z = 302.5\t-7.90254051855962e-19\t1.67197231393762e-18\n+m/z = 302.58\t-2.54806306921044e-18\t4.84666648270261e-18\n+m/z = 302.67\t0.00238735543431953\t0.00059717760153527\n+m/z = 302.75\t0.0422753281275894\t0.0105748304975569\n+m/z = 302.83\t0.0478251463644703\t0.0119630725230272\n+m/z = 302.92\t0.0117873138328592\t0.00294850096557018\n m/z = 303\t0.0005438918878132'..b'.0144305240873075\n+m/z = 395.25\t-0.00378465244012699\t0.00431884573343672\n+m/z = 395.33\t-0.000315001652628076\t0.000359463270406603\n+m/z = 395.42\t1.56478579106423e-07\t-4.9832493669199e-06\n+m/z = 395.5\t4.95699913407887e-08\t-1.57861625005459e-06\n+m/z = 395.58\t4.59965931477345e-09\t-1.46481706778349e-07\n+m/z = 395.67\t-8.93363646461732e-07\t1.01945947057533e-06\n+m/z = 395.75\t-5.28499859979223e-07\t6.03096163123705e-07\n+m/z = 395.83\t0.0101721470821755\t0.00254460417531899\n+m/z = 395.92\t0.0901124169298955\t0.0225408899978156\n+m/z = 396\t0.0619057408174025\t0.0154852188209358\n+m/z = 396.08\t0.0120686207083509\t0.00301886756043136\n+m/z = 396.17\t2.13427762585755e-18\t-4.57591641293874e-18\n+m/z = 396.25\t-5.93693477596822e-11\t6.77491676579856e-11\n+m/z = 396.33\t-1.62663136152525e-11\t1.85622572248383e-11\n+m/z = 396.42\t-1.09391652965735e-12\t1.24832003417318e-12\n+m/z = 396.5\t6.43609376126285e-06\t1.60993663686421e-06\n+m/z = 396.58\t2.04220500508587e-06\t5.10841013808235e-07\n+m/z = 396.67\t1.90042568568878e-07\t4.75376068364845e-08\n+m/z = 396.75\t-4.67251518868319e-15\t5.33097853187915e-15\n+m/z = 396.83\t-2.35613979840554e-15\t2.69012387669633e-15\n+m/z = 396.92\t-3.61561868840093e-16\t4.1275441396577e-16\n+m/z = 397\t0.00683320944088087\t0.00170927192743568\n+m/z = 397.08\t0.0508156173515183\t0.0127111145890864\n+m/z = 397.17\t0.0315399671799999\t0.00788946701538054\n+m/z = 397.25\t0.00571098525966419\t0.00142855664922875\n+m/z = 397.33\t4.89969485396192e-19\t-1.19060334525639e-18\n+m/z = 397.42\t2.22834919338454e-18\t-4.34732897976762e-18\n+m/z = 397.5\t8.31147483196322e-19\t-1.78218120586324e-18\n+m/z = 397.58\t7.14897520004991e-19\t-1.54051878724343e-18\n+m/z = 397.67\t3.41887735034728e-06\t8.55204443656831e-07\n+m/z = 397.75\t1.0035305688935e-06\t2.51025033637385e-07\n+m/z = 397.83\t8.01158365214818e-08\t2.00403268096558e-08\n+m/z = 397.92\t-1.9142113485302e-18\t3.69209812345875e-18\n+m/z = 398\t-2.33556706483865e-18\t4.5182654397614e-18\n+m/z = 398.08\t-0.00206607196679601\t0.00235769234822122\n+m/z = 398.17\t-0.0225874349565933\t0.0257755896848458\n+m/z = 398.25\t-0.0160218359330536\t0.0182832742502864\n+m/z = 398.33\t-0.0026940895995632\t0.00307435297682499\n+m/z = 398.42\t-3.76104775049341e-18\t8.41246115765971e-18\n+m/z = 398.5\t2.39548120740311e-20\t-5.08280982949083e-20\n+m/z = 398.58\t5.66389784439603e-19\t-1.12520168973942e-18\n m/z = 398.67\t0.00295354336564466\t0.0016465989339032\n-m/z = 398.75\t0.100753555082997\t0.0424027103707125\n-m/z = 398.83\t0.0858729519853828\t0.0359862357359943\n-m/z = 398.92\t0.0173733382364935\t0.00713147150476629\n-m/z = 399\t-3.57451534230662e-19\t-1.59668261771468e-19\n-m/z = 399.08\t-3.87913201826644e-19\t-1.67215796549804e-19\n-m/z = 399.17\t1.67250347151359e-18\t7.67055306287817e-19\n-m/z = 399.25\t-3.17057147286199e-18\t-1.35524391550376e-18\n-m/z = 399.33\t8.72598113342265e-06\t3.70432674671029e-06\n-m/z = 399.42\t2.88619885891342e-06\t1.19693828706757e-06\n-m/z = 399.5\t2.87745593748573e-07\t1.14900342935486e-07\n-m/z = 399.58\t-5.56110704789695e-20\t-1.93184342212207e-20\n-m/z = 399.67\t-9.71257164705583e-20\t-3.69674252065695e-20\n-m/z = 399.75\t1.34977946718752e-18\t6.39160896239172e-19\n-m/z = 399.83\t5.28798132613708e-10\t2.33513649004285e-10\n-m/z = 399.92\t3.87854516291594e-10\t1.62263519345642e-10\n+m/z = 398.75\t0.100753555082997\t0.0424027103707126\n+m/z = 398.83\t0.0858729519853825\t0.0359862357359944\n+m/z = 398.92\t0.0173733382364934\t0.00713147150476632\n+m/z = 399\t4.58678491672166e-19\t-1.05711764259232e-18\n+m/z = 399.08\t-3.74124159573477e-18\t8.10123796770424e-18\n+m/z = 399.17\t1.44107919235719e-18\t-2.94492407411307e-18\n+m/z = 399.25\t-2.28306806332197e-18\t4.56015944945022e-18\n+m/z = 399.33\t8.7259811334237e-06\t3.70432674670869e-06\n+m/z = 399.42\t2.88619885891337e-06\t1.19693828706317e-06\n+m/z = 399.5\t2.87745593745991e-07\t1.14900342939911e-07\n+m/z = 399.58\t3.43909756603207e-18\t-7.1235425369153e-18\n+m/z = 399.67\t5.41775952563231e-19\t-1.17632377804067e-18\n+m/z = 399.75\t-2.94880449307325e-20\t5.68563417987762e-20\n+m/z = 399.83\t5.28798133253926e-10\t2.33513647021011e-10\n+m/z = 399.92\t3.87854520523766e-10\t1.62263513454245e-10\n' |
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| diff -r adfef12c7e31 -r 4a62874c21a3 test-data/pca_imzml.pdf |
| b |
| Binary file test-data/pca_imzml.pdf has changed |
| b |
| diff -r adfef12c7e31 -r 4a62874c21a3 test-data/scores_pca.tabular --- a/test-data/scores_pca.tabular Fri Jul 06 14:14:27 2018 -0400 +++ b/test-data/scores_pca.tabular Wed Aug 22 13:44:28 2018 -0400 |
| b |
| @@ -1,10 +1,10 @@ - PC1 PC2 -x = 1, y = 1 1.00970093989579 0.757987492163088 -x = 2, y = 1 0.579669229309751 -0.365615195586665 -x = 3, y = 1 -1.04790449059336 0.831141108678227 -x = 1, y = 2 3.5004093695087 0.608578545994509 -x = 2, y = 2 -0.32505082476202 0.275854508943195 -x = 3, y = 2 -1.31374997886227 0.0192699346592603 -x = 1, y = 3 -1.46193831394871 -0.0337353199555226 -x = 2, y = 3 -1.08833133183904 1.1646109051122 -x = 3, y = 3 0.147195401291164 -3.25809198000829 +pixel names PC1 PC2 +x = 1, y = 1 1.00970093989579 0.757987492163095 +x = 2, y = 1 0.579669229309751 -0.365615195586663 +x = 3, y = 1 -1.04790449059337 0.831141108678224 +x = 1, y = 2 3.5004093695087 0.608578545994517 +x = 2, y = 2 -0.325050824762022 0.275854508943195 +x = 3, y = 2 -1.31374997886227 0.0192699346592569 +x = 1, y = 3 -1.46193831394872 -0.0337353199555284 +x = 2, y = 3 -1.08833133183905 1.16461090511219 +x = 3, y = 3 0.147195401291175 -3.25809198000829 |
| b |
| diff -r adfef12c7e31 -r 4a62874c21a3 test-data/toplabels_skm.tabular --- a/test-data/toplabels_skm.tabular Fri Jul 06 14:14:27 2018 -0400 +++ b/test-data/toplabels_skm.tabular Wed Aug 22 13:44:28 2018 -0400 |
| b |
| @@ -1,21 +1,21 @@ - mz r k cluster centers withinss betweenss -1 1199.55615234375 3 3 1 37 0 3661.33333333333 -2 1199.55615234375 3 3 2 12.3333333333333 154 3661.33333333333 -3 1199.55615234375 3 3 3 81 18.6666666666667 3661.33333333333 -4 1199.59753417969 3 3 1 34.6 0 3658.13333333333 -5 1199.59753417969 3 3 2 14.3333333333333 137.2 3658.13333333333 -6 1199.59753417969 3 3 3 84 144.666666666667 3658.13333333333 -7 1199.55615234375 1 3 1 39.3333333333333 18.6666666666667 2198 -8 1199.55615234375 1 3 2 12.3333333333333 112.666666666667 2198 -9 1199.55615234375 1 3 3 49.3333333333333 1504.66666666667 2198 -10 1199.55615234375 2 3 1 39.3333333333333 18.6666666666667 2198 -11 1199.55615234375 2 3 2 12.3333333333333 112.666666666667 2198 -12 1199.55615234375 2 3 3 49.3333333333333 1504.66666666667 2198 -13 1199.63891601562 3 3 1 30.4 0 2049.02222222222 -14 1199.63891601562 3 3 2 11 45.2 2049.02222222222 -15 1199.63891601562 3 3 3 62 26 2049.02222222222 -16 1199.55615234375 2 2 1 44.3333333333333 18.6666666666667 2048 -17 1199.55615234375 2 2 2 12.3333333333333 1767.33333333333 2048 -18 1199.55615234375 3 2 1 44.3333333333333 18.6666666666667 2048 -19 1199.55615234375 3 2 2 12.3333333333333 1767.33333333333 2048 -20 1199.59753417969 1 3 1 37.6666666666667 144.666666666667 1784.66666666667 +mz r k cluster centers withinss betweenss +1199.55615234375 3 3 1 81 154 3661.33333333333 +1199.55615234375 3 3 2 12.3333333333333 18.6666666666667 3661.33333333333 +1199.55615234375 3 3 3 37 0 3661.33333333333 +1199.59753417969 3 3 1 84 137.2 3658.13333333333 +1199.59753417969 3 3 2 14.3333333333333 144.666666666667 3658.13333333333 +1199.59753417969 3 3 3 34.6 0 3658.13333333333 +1199.55615234375 1 3 1 49.3333333333333 1504.66666666667 2198 +1199.55615234375 1 3 2 12.3333333333333 112.666666666667 2198 +1199.55615234375 1 3 3 39.3333333333333 18.6666666666667 2198 +1199.55615234375 2 3 1 49.3333333333333 1504.66666666667 2198 +1199.55615234375 2 3 2 12.3333333333333 112.666666666667 2198 +1199.55615234375 2 3 3 39.3333333333333 18.6666666666667 2198 +1199.63891601562 3 3 1 62 45.2 2049.02222222222 +1199.63891601562 3 3 2 11 26 2049.02222222222 +1199.63891601562 3 3 3 30.4 0 2049.02222222222 +1199.55615234375 2 2 1 44.3333333333333 1767.33333333333 2048 +1199.55615234375 2 2 2 12.3333333333333 18.6666666666667 2048 +1199.55615234375 3 2 1 44.3333333333333 1767.33333333333 2048 +1199.55615234375 3 2 2 12.3333333333333 18.6666666666667 2048 +1199.59753417969 1 3 1 48 1946 1784.66666666667 |
| b |
| diff -r adfef12c7e31 -r 4a62874c21a3 test-data/toplabels_ssc.tabular --- a/test-data/toplabels_ssc.tabular Fri Jul 06 14:14:27 2018 -0400 +++ b/test-data/toplabels_ssc.tabular Wed Aug 22 13:44:28 2018 -0400 |
| b |
| @@ -1,51 +1,51 @@ - mz r k s classes centers tstatistics p.values adj.p.values -1 364.333343505859 1 3 2 1 15.8337765722821 0.449479909587349 NA NA -2 364.333343505859 2 3 2 1 15.8337765722821 0.449479909587349 NA NA -3 203.833343505859 1 3 2 1 14.0415253451331 0.449478654505296 NA NA -4 203.833343505859 2 3 2 1 14.0415253451331 0.449478654505296 NA NA -5 259.916656494141 1 3 2 1 13.8981327063543 0.449478540011514 NA NA -6 259.916656494141 2 3 2 1 13.8981327063543 0.449478540011514 NA NA -7 200.25 1 3 2 1 10.4880169699887 0.449474897701911 NA NA -8 200.25 2 3 2 1 10.4880169699887 0.449474897701911 NA NA -9 200.333343505859 1 3 2 1 10.2892503590812 0.449474610932727 NA NA -10 200.333343505859 2 3 2 1 10.2892503590812 0.449474610932727 NA NA -11 259.833343505859 1 3 2 1 9.55638913925806 0.449473448172064 NA NA -12 259.833343505859 2 3 2 1 9.55638913925806 0.449473448172064 NA NA -13 360.916687011719 1 3 2 1 9.04224883162212 0.449472524177856 NA NA -14 360.916687011719 2 3 2 1 9.04224883162212 0.449472524177856 NA NA -15 370.083343505859 1 3 2 1 8.45643021892373 0.44947133139287 NA NA -16 370.083343505859 2 3 2 1 8.45643021892373 0.44947133139287 NA NA -17 364.25 1 3 2 1 8.15357261143537 0.449470647536679 NA NA -18 364.25 2 3 2 1 8.15357261143537 0.449470647536679 NA NA -19 200.16667175293 1 3 2 1 6.16326174971333 0.449464481313509 NA NA -20 200.16667175293 2 3 2 1 6.16326174971333 0.449464481313509 NA NA -21 203.91667175293 1 3 2 1 6.03716112636297 0.449463953687195 NA NA -22 203.91667175293 2 3 2 1 6.03716112636297 0.449463953687195 NA NA -23 225 1 3 2 1 5.71436916011582 0.449462496977867 NA NA -24 225 2 3 2 1 5.71436916011582 0.449462496977867 NA NA -25 216.91667175293 1 3 2 1 5.64877209898622 0.449462180580643 NA NA -26 216.91667175293 2 3 2 1 5.64877209898622 0.449462180580643 NA NA -27 249.25 1 3 2 1 5.15263210866428 0.449459526788925 NA NA -28 249.25 2 3 2 1 5.15263210866428 0.449459526788925 NA NA -29 367.583343505859 1 3 2 1 4.44314020180342 0.449454702074192 NA NA -30 367.583343505859 2 3 2 1 4.44314020180342 0.449454702074192 NA NA -31 364.416687011719 1 3 2 1 4.30740701190317 0.449453597945591 NA NA -32 364.416687011719 2 3 2 1 4.30740701190317 0.449453597945591 NA NA -33 370 1 3 2 1 4.15967192336677 0.449452314295502 NA NA -34 370 2 3 2 1 4.15967192336677 0.449452314295502 NA NA -35 249.333343505859 1 3 2 1 4.06900916364662 0.449451480388054 NA NA -36 249.333343505859 2 3 2 1 4.06900916364662 0.449451480388054 NA NA -37 260 1 3 2 1 4.06636831188445 0.449451455520709 NA NA -38 260 2 3 2 1 4.06636831188445 0.449451455520709 NA NA -39 361 1 3 2 1 3.70261707034987 0.449447694373555 NA NA -40 361 2 3 2 1 3.70261707034987 0.449447694373555 NA NA -41 250.583343505859 1 3 2 1 3.44558838817237 0.449444557922452 NA NA -42 250.583343505859 2 3 2 1 3.44558838817237 0.449444557922452 NA NA -43 360.833343505859 1 3 2 1 3.35278414565422 0.449443307303055 NA NA -44 360.833343505859 2 3 2 1 3.35278414565422 0.449443307303055 NA NA -45 370.166687011719 1 3 2 1 2.82853938684749 0.449434701602457 NA NA -46 370.166687011719 2 3 2 1 2.82853938684749 0.449434701602457 NA NA -47 367.666687011719 1 3 2 1 2.5012261861986 0.449427499520948 NA NA -48 367.666687011719 2 3 2 1 2.5012261861986 0.449427499520948 NA NA -49 225.083343505859 1 3 2 1 2.45608703725853 0.449426355692286 NA NA -50 225.083343505859 2 3 2 1 2.45608703725853 0.449426355692286 NA NA +mz r k s classes centers tstatistics p.values adj.p.values +364.333343505859 1 3 2 1 15.8337765722821 0.449479909587349 NA NA +364.333343505859 2 3 2 1 15.8337765722821 0.449479909587349 NA NA +203.833343505859 1 3 2 1 14.0415253451331 0.449478654505296 NA NA +203.833343505859 2 3 2 1 14.0415253451331 0.449478654505296 NA NA +259.916656494141 1 3 2 1 13.8981327063543 0.449478540011514 NA NA +259.916656494141 2 3 2 1 13.8981327063543 0.449478540011514 NA NA +200.25 1 3 2 1 10.4880169699887 0.449474897701911 NA NA +200.25 2 3 2 1 10.4880169699887 0.449474897701911 NA NA +200.333343505859 1 3 2 1 10.2892503590812 0.449474610932727 NA NA +200.333343505859 2 3 2 1 10.2892503590812 0.449474610932727 NA NA +259.833343505859 1 3 2 1 9.55638913925806 0.449473448172064 NA NA +259.833343505859 2 3 2 1 9.55638913925806 0.449473448172064 NA NA +360.916687011719 1 3 2 1 9.04224883162212 0.449472524177856 NA NA +360.916687011719 2 3 2 1 9.04224883162212 0.449472524177856 NA NA +370.083343505859 1 3 2 1 8.45643021892373 0.44947133139287 NA NA +370.083343505859 2 3 2 1 8.45643021892373 0.44947133139287 NA NA +364.25 1 3 2 1 8.15357261143537 0.449470647536679 NA NA +364.25 2 3 2 1 8.15357261143537 0.449470647536679 NA NA +200.16667175293 1 3 2 1 6.16326174971333 0.449464481313509 NA NA +200.16667175293 2 3 2 1 6.16326174971333 0.449464481313509 NA NA +203.91667175293 1 3 2 1 6.03716112636297 0.449463953687195 NA NA +203.91667175293 2 3 2 1 6.03716112636297 0.449463953687195 NA NA +225 1 3 2 1 5.71436916011582 0.449462496977867 NA NA +225 2 3 2 1 5.71436916011582 0.449462496977867 NA NA +216.91667175293 1 3 2 1 5.64877209898622 0.449462180580643 NA NA +216.91667175293 2 3 2 1 5.64877209898622 0.449462180580643 NA NA +249.25 1 3 2 1 5.15263210866428 0.449459526788925 NA NA +249.25 2 3 2 1 5.15263210866428 0.449459526788925 NA NA +367.583343505859 1 3 2 1 4.44314020180342 0.449454702074192 NA NA +367.583343505859 2 3 2 1 4.44314020180342 0.449454702074192 NA NA +364.416687011719 1 3 2 1 4.30740701190317 0.449453597945591 NA NA +364.416687011719 2 3 2 1 4.30740701190317 0.449453597945591 NA NA +370 1 3 2 1 4.15967192336677 0.449452314295502 NA NA +370 2 3 2 1 4.15967192336677 0.449452314295502 NA NA +249.333343505859 1 3 2 1 4.06900916364662 0.449451480388054 NA NA +249.333343505859 2 3 2 1 4.06900916364662 0.449451480388054 NA NA +260 1 3 2 1 4.06636831188445 0.449451455520709 NA NA +260 2 3 2 1 4.06636831188445 0.449451455520709 NA NA +361 1 3 2 1 3.70261707034987 0.449447694373555 NA NA +361 2 3 2 1 3.70261707034987 0.449447694373555 NA NA +250.583343505859 1 3 2 1 3.44558838817237 0.449444557922452 NA NA +250.583343505859 2 3 2 1 3.44558838817237 0.449444557922452 NA NA +360.833343505859 1 3 2 1 3.35278414565422 0.449443307303055 NA NA +360.833343505859 2 3 2 1 3.35278414565422 0.449443307303055 NA NA +370.166687011719 1 3 2 1 2.82853938684749 0.449434701602457 NA NA +370.166687011719 2 3 2 1 2.82853938684749 0.449434701602457 NA NA +367.666687011719 1 3 2 1 2.5012261861986 0.449427499520948 NA NA +367.666687011719 2 3 2 1 2.5012261861986 0.449427499520948 NA NA +225.083343505859 1 3 2 1 2.45608703725853 0.449426355692286 NA NA +225.083343505859 2 3 2 1 2.45608703725853 0.449426355692286 NA NA |