| Previous changeset 1:ae9ffc7ba261 (2018-10-25) Next changeset 3:16556ca0196b (2019-02-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 |
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modified:
macros.xml quality_report.xml test-data/112_auto_combined_QC.pdf test-data/123_combined.RData test-data/123_combined_QC.pdf test-data/12_combined.RData test-data/12_combined_QC.pdf test-data/2123_auto_combined.RData test-data/2123_auto_combined_QC.pdf test-data/Plot_empty_spectra.pdf test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf test-data/analyze75_filtered2.pdf test-data/centroids_rdata.pdf test-data/cluster_skm.RData test-data/features_test2.tabular test-data/features_test4.tabular test-data/features_test6.tabular test-data/features_test7.tabular test-data/imzml_filtered3.pdf test-data/imzml_filtered4.pdf test-data/imzml_filtered5.pdf test-data/kmeans_analyze.pdf test-data/pca_imzml.pdf test-data/pixel_out2.tabular test-data/pixel_out3.tabular test-data/preprocessing_results1.pdf test-data/preprocessing_results2.pdf test-data/preprocessing_results3.pdf test-data/preprocessing_results4.pdf test-data/preprocessing_results5.RData test-data/preprocessing_results5.pdf test-data/rdata_notfiltered.pdf test-data/scores_pca.tabular test-data/test1.pdf test-data/test2.pdf test-data/test2.rdata test-data/test3.pdf test-data/test4.pdf test-data/test4.rdata test-data/test5.pdf test-data/test6.pdf test-data/test6.rdata test-data/test7.pdf test-data/test7.rdata |
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added:
test-data/112_auto_combined.ibd test-data/112_auto_combined.imzml test-data/112_auto_combined.imzml.txt test-data/123_annotation.ibd test-data/123_annotation.imzml test-data/123_auto_combined.imzml.txt test-data/123_combined_auto.ibd test-data/123_combined_auto.imzml test-data/123_combined_auto.imzml.txt test-data/123_combined_auto.pdf test-data/123_combined_auto.tabular test-data/out3.ibd test-data/out3.imzml test-data/out3.imzml.txt test-data/out4.ibd test-data/out4.imzml test-data/out4.imzml.txt test-data/out5.ibd test-data/out5.imzml test-data/out5.imzml.txt test-data/out6.ibd test-data/out6.imzml test-data/out6.imzml.txt test-data/out7.ibd test-data/out7.imzml test-data/out7.imzml.txt test-data/preprocessing_results1.ibd test-data/preprocessing_results1.imzml test-data/preprocessing_results1.imzml.txt test-data/preprocessing_results2.ibd test-data/preprocessing_results2.imzml test-data/preprocessing_results2.imzml.txt test-data/preprocessing_results3.ibd test-data/preprocessing_results3.imzml test-data/preprocessing_results3.imzml.txt test-data/preprocessing_results4.ibd test-data/preprocessing_results4.imzml test-data/preprocessing_results4.imzml.txt |
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removed:
test-data/112_auto_combined.RData test-data/analyze_filtered.RData test-data/analyze_filtered.pdf test-data/analyze_filteredoutside.RData test-data/analyze_originaloutput.RData test-data/analyze_originaloutput2.RData test-data/imzml_filtered.RData test-data/imzml_filtered.pdf test-data/imzml_filtered3.RData test-data/imzml_filtered4.RData test-data/imzml_filtered5.RData test-data/loadings_pca.tabular test-data/preprocessed.rdata test-data/preprocessing_results1.RData test-data/preprocessing_results1.txt test-data/preprocessing_results2.RData test-data/preprocessing_results2.txt test-data/preprocessing_results3.RData test-data/preprocessing_results4.RData test-data/preprocessing_results4.txt test-data/preprocessing_results5.txt test-data/rdata_notfiltered.RData |
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| diff -r ae9ffc7ba261 -r d4803c1e5e19 macros.xml --- a/macros.xml Thu Oct 25 07:28:42 2018 -0400 +++ b/macros.xml Fri Feb 15 10:21:09 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) + ]]></token> + + <token name="@READING_MSIDATA_INRAM@"><![CDATA[ + ## importing MSI data files + + ## function to read RData files independent of filename + loadRData <- function(fileName){ + load(fileName) + get(ls()[ls() != "fileName"]) + } + + #if $infile.ext == 'imzml' + #if str($processed_cond.processed_file) == "processed": + msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units") + centroided(msidata) = $centroids + #else + msidata <- readImzML('infile') + centroided(msidata) = $centroids + #end if + #elif $infile.ext == 'analyze75' + msidata = readAnalyze('infile') + centroided(msidata) = $centroids + #else + msidata = loadRData('infile.RData') + #end if + + ]]></token> + + <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[ +########################### QC numbers ######################## +## including intensity calculations which need data in RAM + ## Number of features (mz) + maxfeatures = length(features(msidata)) + ## Range mz + minmz = round(min(mz(msidata)), digits=2) + maxmz = round(max(mz(msidata)), digits=2) + ## Number of spectra (pixels) + pixelcount = length(pixels(msidata)) + ## Range x coordinates + minimumx = min(coord(msidata)[,1]) + maximumx = max(coord(msidata)[,1]) + ## Range y coordinates + minimumy = min(coord(msidata)[,2]) + maximumy = max(coord(msidata)[,2]) ## Range of intensities minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2) maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2) ## Number of intensities > 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) ]]></token> @@ -144,9 +211,9 @@ <token name="@SPECTRA_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ - Optional file with pixel coordinates and annotation: - - Tabular file: One column with x values, one column wiht y values and one column with annotations + - Tabular file: One column with x values, one column with y values and one column with annotations - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes) - - Pixel with coordinates outside the coordinates of the input file are ignored + - Pixel with coordinates outside the coordinates of the input file are ignored :: @@ -161,9 +228,9 @@ <xml name="reading_msidata"> <param name="infile" type="data" format="imzml,rdata,analyze75" - label="Input file as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData" - help="Upload composite datatype imzML (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/> - <param name="centroids" type="boolean" label="Is the input data centroided (picked)" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/> + label="MSI data" + help="Input file as imzML (composite upload), or Cardinal MSImageSet saved as RData (regular upload)"/> + <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/> <conditional name="processed_cond"> <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file"> <option value="no_processed" selected="True">no</option> |
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| diff -r ae9ffc7ba261 -r d4803c1e5e19 quality_report.xml --- a/quality_report.xml Thu Oct 25 07:28:42 2018 -0400 +++ b/quality_report.xml Fri Feb 15 10:21:09 2019 -0500 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="cardinal_quality_report" name="MSI Qualitycontrol" version="@VERSION@.1">\n+<tool id="cardinal_quality_report" name="MSI Qualitycontrol" version="@VERSION@.2">\n <description>\n mass spectrometry imaging QC\n </description>\n@@ -34,15 +34,15 @@\n library(pheatmap)\n \n \n-@READING_MSIDATA@\n+@READING_MSIDATA_INRAM@\n+\n+## create full matrix to make processed imzML files compatible with segmentation and other steps\n+iData(msidata) <- iData(msidata)[]\n \n ## remove duplicated coordinates\n print(paste0(sum(duplicated(coord(msidata))), " duplicated coordinates were removed"))\n msidata <- msidata[,!duplicated(coord(msidata))]\n \n-## create full matrix to make processed imzML files compatible with segmentation and other steps\n-iData(msidata) <- iData(msidata)[]\n-\n ## optional annotation from tabular file to obtain pixel groups (otherwise all pixels are considered to be one sample)\n \n #if str($tabular_annotation.load_annotation) == \'yes_annotation\':\n@@ -64,12 +64,12 @@\n #end if\n \n ###################### calculation of data properties ################################\n-@DATA_PROPERTIES@\n+@DATA_PROPERTIES_INRAM@\n \n ## Median intensities\n medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)\n ## Spectra multiplied with m/z (potential number of peaks)\n-numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])\n+numpeaks = ncol(msidata)*nrow(msidata)\n ## Percentage of intensities > 0\n percpeaks = round(npeaks/numpeaks*100, digits=2)\n ## Number of empty TICs\n@@ -81,17 +81,16 @@\n ## Median and sd # peaks per spectrum\n medpeaks = round(median(colSums(spectra(msidata)[]>0, na.rm=TRUE), na.rm=TRUE), digits=0)\n sdpeaks = round(sd(colSums(spectra(msidata)[]>0, na.rm=TRUE), na.rm=TRUE), digits=0)\n-print(cor(TICs,colSums(spectra(msidata)[]>0), method="pearson"))\n ## Processing informations\n centroidedinfo = centroided(msidata)\n \n ############## Read and filter tabular file with m/z ###########################\n \n-### reading calibrant file: \n+### reading m/z input (calibrant) file:\n \n #if $calibrant_file:\n \n- calibrant_list = read.delim("$calibrant_file", header = $calibrant_header, na.strings=c("","NA"), stringsAsFactors = FALSE)\n+ calibrant_list = read.delim("$calibrant_file", header = $calibrant_header, na.strings=c(" ","","NA"), stringsAsFactors = FALSE)\n calibrant_list = calibrant_list[,c($mz_column, $name_column)]\n \n ### calculate how many input calibrant m/z are valid: \n@@ -138,7 +137,7 @@\n "Median TIC \xc2\xb1 sd", \n "Median # peaks per spectrum \xc2\xb1 sd",\n "Centroided", \n- paste0("calibrants (#valid/#input) in \\n", "$calibrant_file.display_name"))\n+ paste0("input m/z (#valid/#input) in \\n", "$calibrant_file.display_name"))\n \n values2 = c(paste0(medint),\n paste0(percpeaks, " %"), \n@@ -161,7 +160,9 @@\n print("x-y images")\n \n ## only do plots for file with intensity peaks\n+\n if (npeaks > 0){\n+\n ## function for density plots\n plot_colorByDensity = function(x1,x2,\n ylim=c(min(x2),max(x2)),\n@@ -204,8 +205,11 @@\n colnames(pixel_name_df) = c("pixel_number", "pixel_name")\n last_pixel = aggregate(pixel_number~pixel_name, data = pixel_name_df, max)\n pixel_vector = last_pixel[,2]\n- abline_vector = pixel_vector[1:number_combined-1]\n- print(abline_vector)\n+ abline_vector = pixel_vector\n+\n+ ## remove position_df to clean up RAM space\n+ rm(position_df)\n+ gc()\n }\n \n ################### 1) Pixel order image ###################################\n@@ -220,7 +224,11 @@\n theme(plot.title = element_text(hjust = 0.5))+\n theme(text=element_text(family="ArialMT", face="bold", size=12))+\n scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"), \n- space = "Lab", na.value = "black", name = "Pixel\\nnumber"))\n+ space = "Lab", na.value = "black", name = "Pixel\\nnumber"))\n+\n+ ## rem'..b'er spectrum and annotation group: Same histogram as in plot before but with colours to show the contribution of each pixel annotation group. Only the length of the coloured bar is important and not its height from zero, as bars are added up and not overlayed. \n \n **Properties over m/z features**\n \n@@ -980,19 +1088,20 @@\n **Intensity plots**\n \n - Median intensity per spectrum: Scatter plot in which each point represents the median intensity for one spectrum. Dotted lines in the scatter plot separate spectra of different annotation groups.\n-- Log2-transformed intensities: Histogram of log2-transformed intensities. \n-- (annot) log2-transformed intensities per annotation group: Same histogram as before but with colours to show the contribution of each pixel annotation group. \n+- Histogram of intensities. \n+- (annot) Intensities per annotation group: Same histogram as before but with colours to show the contribution of each pixel annotation group. \n - (annot) Mean intensities per m/z and annotation group: For all pixels of an annotation group the mean intensity for each m/z is calculated and shown as boxplot. \n-- (annot) Pearson correlation between annotation groups based on mean intensities and shown as heatmap.\n+- (annot) Pearson correlation between annotation groups (needs at least 2 groups) based on mean intensities and shown as heatmap.\n \n **Mass spectra and m/z accuracy**\n \n-- Mass spectra over the full m/z range: First plot shows the average intensities over all spectra. The other three mass spectra are from random individual pixels (spectra). \n-- (cal) For each calibrant four zoomed in mass spectrum are drawn: The first two mass spectra show the average intensities over all spectra and the other two specra are from random individual pixels. The theoretical calibrant m/z (taken from the input file) is represented by the dashed blue line. The dotted blue lines show the given ppm range. The green line is the m/z value that is closest to the theoretical calibrant and the red line is the m/z with the highest average intensity in the m/z window. In the second average spectra plot each blue plot indicates one data point.\n+- Average mass spectra: First plot shows the average spectrum over the full m/z range, the other three plots zoom into the m/z axis.\n+- (cal) For each calibrant four zoomed average mass spectrum are drawn with different zooming level. The theoretical calibrant m/z (taken from the input file) is represented by the dashed blue line. The dotted blue lines show the given ppm range. The green line is the m/z value that is closest to the theoretical calibrant and the red line is the m/z with the highest average intensity in the m/z window. In the second spectrum each blue dot indicates one data point.\n - (annot) Average spectrum per annotation group: For each calibrant a zoomed in mass spectrum is plotted this time with the average intensities for each annotation group separately. \n - (cal) Difference m/z with max. average intensity vs. theor. calibrant m/z: The difference in ppm between the m/z with the highest average intensity and the theoretical m/z are plotted for each calibrant. This corresponds to the difference between the dashed blue line and the red line in the zoomed in mass spectra. \n - (cal) Difference closest measured m/z vs. theor. calibrant m/z: The difference in ppm between the closest m/z value and the theoretical m/z values are plotted for each calibrant. This corresponds to the difference between the dashed blue line and the green line in the zoomed in mass spectra. \n - (cal) Difference m/z with max. average intensity vs. theor. m/z (per spectrum): For each spectrum the ppm difference between the m/z with the highest average intensity and the theoretical m/z are plotted. The calibrants have different plotting colours. Dashed lines separate spectra of different annotation groups. \n+- (cal) Same m/z accuracy in ppm is plotted per calibrant and per spectrum as image in x-y dimension.\n \n \n ]]>\n' |
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| diff -r ae9ffc7ba261 -r d4803c1e5e19 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 10:21:09 2019 -0500 |
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| b'@@ -0,0 +1,475 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally 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|
| b |
| diff -r ae9ffc7ba261 -r d4803c1e5e19 test-data/features_test4.tabular --- a/test-data/features_test4.tabular Thu Oct 25 07:28:42 2018 -0400 +++ b/test-data/features_test4.tabular Fri Feb 15 10:21:09 2019 -0500 |
| b |
| b'@@ -1,101 +1,101 @@\n 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\t0.001177\t0.025661\t0.036479\n+922.319458007812\t3\tA\t0.001163\t0.035058\t0.049004\n+945.825500488281\t3\tA\t0.001163\t0.035839\t0.039942\n+914.429443359375\t3\tA\t0.001148\t0.021433\t0.032258\n+934.364013671875\t3\tA\t0.00112\t0.026118\t0.02779\n+945.788757324219\t3\tA\t0.001114\t0.060266\t0.067849\n+930.27978515625\t3\tA\t0.001111\t0.054857\t0.054186\n+987.41015625\t3\tA\t0.001091\t0.025902\t0.034883\n+917.320922851562\t3\tB\t0.001088\t-0.038094\t-0.085973\n+961.388977050781\t3\tA\t0.001083\t0.020899\t0.023595\n+949.244445800781\t3\tA\t0.001081\t0.055346\t0.047329\n+914.393310546875\t3\tA\t0.001079\t0.018641\t0.021345\n+923.37158203125\t3\tA\t0.001074\t0.017416\t0.030093\n+967.322998046875\t3\tA\t0.001062\t0.041383\t0.029151\n+961.314880371094\t3\tA\t0.001057\t0.042956\t0.034557\n+994.252197265625\t3\tA\t0.001053\t0.04654\t0.044418\n+945.348083496094\t3\tA\t0.001048\t0.004905\t0.005537\n+913.346313476562\t3\tA\t0.001035\t0.018956\t0.026733\n+914.321105957031\t3\tA\t0.00103\t0.028293\t0.028426\n+929.442138671875\t3\tA\t0.001024\t0.022905\t0.027626\n+922.42822265625\t3\tA\t0.00102\t0.004391\t0.022483\n+978.386474609375\t3\tA\t0.001011\t0.047712\t0.031523\n+939.335510253906\t3\tA\t0.00101\t0.011529\t0.021342\n+929.478515625\t3\tA\t0.00101\t0.037604\t0.039359\n+939.079284667969\t3\tA\t0.001008\t0.03122\t0.044202\n+943.843139648438\t3\tA\t0.000999\t0.02673\t0.036566\n+929.842712402344\t3\tA\t0.000986\t0.083195\t0.108038\n+940.397277832031\t3\tA\t0.000981\t0.015143\t0.027754\n+990.302001953125\t3\tA\t0.000975\t0.039464\t0.035796\n+913.310180664062\t3\tA\t0.000969\t0.010782\t0.026242\n+912.3359375\t3\tA\t0.000967\t0.03343\t0.026227\n+934.327514648438\t3\tA\t0.000965\t0.038056\t0.024783\n+978.34912109375\t3\tA\t0.000952\t0.024638\t0.026361\n+964.427856445312\t3\tA\t0.00095\t0.020628\t0.032363\n+905.135498046875\t3\tA\t0.000939\t0.035836\t0.046276\n+902.9091796875\t3\tA\t0.000928\t0.027048\t0.033126\n+970.296875\t3\tA\t0.000918\t0.041289\t0.037105\n+900.291320800781\t3\tA\t0.000916\t0.036901\t0.029943\n+936.372924804688\t3\tA\t0.000914\t0.03047\t0.017231\n+902.550354003906\t3\tA\t0.000913\t0.020687\t0.031436\n+969.329895019531\t3\tA\t0.000909\t0.03814\t0.02905\n+928.350158691406\t3\tB\t0.000901\t-0.035429\t-0.078124\n+906.465454101562\t3\tA\t0.000895\t0.027815\t0.004156\n+951.195617675781\t3\tA\t0.00089\t0.021378\t0.039051\n+929.296508789062\t3\tA\t0.000889\t0.057417\t0.040791\n+910.389038085938\t3\tA\t0.000889\t0.008833\t0.02408\n+900.362976074219\t3\tA\t0.000884\t0.060121\t0.020862\n+938.274291992188\t3\tA\t0.000883\t0.042087\t0.028046\n+978.423828125\t3\tA\t0.000873\t0.029626\t0.029782\n+911.326171875\t3\tA\t0.000868\t0.039419\t0.029076\n+931.700927734375\t3\tA\t0.000861\t0.028025\t0.033752\n+974.393371582031\t3\tA\t0.000861\t0.041984\t0.028948\n+948.251220703125\t3\tA\t0.000851\t0.058621\t0.045804\n+930.862670898438\t3\tB\t0.000847\t-0.030159\t-0.041363\n+916.923034667969\t3\tA\t0.000845\t0.020133\t0.031831\n+949.318054199219\t3\tA\t0.000845\t0.031551\t0.027948\n+985.459655761719\t3\tA\t0.000843\t0.029168\t0.029559\n+907.4365234375\t3\tA\t0.000843\t0.024964\t0.017428\n+925.18701171875\t3\tA\t0.000838\t0.02295\t0.022881\n+929.332885742188\t3\tB\t0.000837\t-0.029367\t-0.054765\n+937.506225585938\t3\tA\t0.000834\t0.017846\t0.027822\n+987.335083007812\t3\tA\t0.000833\t0.030891\t0.027528\n+987.372619628906\t3\tA\t0.000826\t0.03863\t0.02261\n+991.392211914062\t3\tA\t0.000822\t0.030112\t0.025841\n+986.359619140625\t3\tA\t0.000817\t0.022246\t0.021413\n+995.608337402344\t3\tA\t0.000815\t0.024475\t0.037252\n+901.438415527344\t3\tB\t0.000812\t-0.144815\t-0.105509\n+927.295166015625\t3\tA\t0.00081\t0.03242\t0.019578\n+957.467712402344\t3\tA\t0.000805\t0.034961\t0.029421\n+982.387756347656\t3\tA\t0.000802\t0.029613\t0.024039\n' |
| b |
| diff -r ae9ffc7ba261 -r d4803c1e5e19 test-data/features_test6.tabular --- a/test-data/features_test6.tabular Thu Oct 25 07:28:42 2018 -0400 +++ b/test-data/features_test6.tabular Fri Feb 15 10:21:09 2019 -0500 |
| b |
| @@ -1,21 +1,21 @@ mz r k s classes centers tstatistics p.values adj.p.values -928.859680175781 2 3 2 B 43.9516959905118 0.541814677313986 0.607464263577403 1 -912.877136230469 2 3 2 B 55.419364071664 0.437808238568372 0.676846169835776 1 -913.887756347656 2 3 2 B 24.9140214890445 0.393340199810185 0.70766449744142 1 -930.862670898438 2 3 2 B 9.28583084091344 0.29858210475084 0.775329712997245 1 -913.923889160156 2 3 2 B 12.1491837287613 0.0960056413112618 0.926642424678888 1 -900.004699707031 2 3 2 A 2.29166666666667 0 1 1 +928.859680175781 2 3 2 B 43.951696 0.541815 0.607464 1 +912.877136230469 2 3 2 B 55.419364 0.437808 0.676846 1 +913.887756347656 2 3 2 B 24.914021 0.39334 0.707664 1 +930.862670898438 2 3 2 B 9.285831 0.298582 0.77533 1 +913.923889160156 2 3 2 B 12.149184 0.096006 0.926642 1 +900.004699707031 2 3 2 A 2.291667 0 1 1 900.04052734375 2 3 2 A 3.125 0 1 1 -900.076354980469 2 3 2 A 3.33333333333333 0 1 1 -900.112182617188 2 3 2 A 3.45833333333333 0 1 1 -900.148010253906 2 3 2 A 3.29166666666667 0 1 1 +900.076354980469 2 3 2 A 3.333333 0 1 1 +900.112182617188 2 3 2 A 3.458333 0 1 1 +900.148010253906 2 3 2 A 3.291667 0 1 1 900.183837890625 2 3 2 A 3.375 0 1 1 -900.219665527344 2 3 2 A 3.66666666666667 0 1 1 -900.255493164062 2 3 2 A 3.91666666666667 0 1 1 -900.291320800781 2 3 2 A 4.08333333333333 0 1 1 -900.3271484375 2 3 2 A 5.79166666666667 0 1 1 -900.362976074219 2 3 2 A 11.5416666666667 0 1 1 -900.398864746094 2 3 2 A 26.2083333333333 0 1 1 -900.434692382812 2 3 2 A 30.0416666666667 0 1 1 -900.470520019531 2 3 2 A 19.1666666666667 0 1 1 +900.219665527344 2 3 2 A 3.666667 0 1 1 +900.255493164062 2 3 2 A 3.916667 0 1 1 +900.291320800781 2 3 2 A 4.083333 0 1 1 +900.3271484375 2 3 2 A 5.791667 0 1 1 +900.362976074219 2 3 2 A 11.541667 0 1 1 +900.398864746094 2 3 2 A 26.208333 0 1 1 +900.434692382812 2 3 2 A 30.041667 0 1 1 +900.470520019531 2 3 2 A 19.166667 0 1 1 900.50634765625 2 3 2 A 8.5 0 1 1 |
| b |
| diff -r ae9ffc7ba261 -r d4803c1e5e19 test-data/features_test7.tabular --- a/test-data/features_test7.tabular Thu Oct 25 07:28:42 2018 -0400 +++ b/test-data/features_test7.tabular Fri Feb 15 10:21:09 2019 -0500 |
| b |
| b'@@ -1,101 +1,101 @@\n 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| diff -r ae9ffc7ba261 -r d4803c1e5e19 test-data/out3.ibd |
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| Binary file test-data/out3.ibd has changed |
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| diff -r ae9ffc7ba261 -r d4803c1e5e19 test-data/out3.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out3.imzml.txt Fri Feb 15 10:21:09 2019 -0500 |
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| @@ -0,0 +1,4 @@ +imzML file: +total 24 +-rw-r--r-- 1 meli meli 9616 Feb 12 19:18 ibd +-rw-r--r-- 1 meli meli 8282 Feb 12 19:18 imzml |
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| diff -r ae9ffc7ba261 -r d4803c1e5e19 test-data/out4.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out4.imzml.txt Fri Feb 15 10:21:09 2019 -0500 |
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| diff -r ae9ffc7ba261 -r d4803c1e5e19 test-data/out5.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out5.imzml.txt Fri Feb 15 10:21:09 2019 -0500 |
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| @@ -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 |
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| @@ -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 -345 0 0 4.70593890744759 0 0 0 5.23000350586712 4.17949067812964 5.08555910047608 |
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| diff -r ae9ffc7ba261 -r d4803c1e5e19 test-data/preprocessing_results4.txt --- a/test-data/preprocessing_results4.txt Thu Oct 25 07:28:42 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,160 +0,0 @@\n-mz\tx = 1, y = 1\tx = 2, y = 1\tx = 3, y = 1\tx = 1, y = 2\tx = 2, y = 2\tx = 3, y = 2\tx = 1, y = 3\tx = 2, y = 3\tx = 3, y = 3\n-1199\t1.90173968313755\t1.13259535967648\t2.08382650993109\t2.34349737625869\t1.33087314662273\t2.14468085106383\t3.43161925601751\t1.32706902782797\t2.22480967308554\n-1200\t1.39388874502695\t0.970046951574763\t1.52152411836238\t1.35619061126081\t1.10906095551895\t1.66382978723404\t2.22846006564551\t1.19804842790025\t1.7089117778773\n-1201\t1.13095882671438\t0.99102093971692\t1.23623834616944\t1.19344773790952\t1.05864909390445\t1.31063829787234\t1.67396061269147\t1.07824358511023\t1.28168383340797\n-1202\t1.09263589067539\t0.976548887898831\t1.13518929874341\t1.0033640618352\t0.953389126853377\t1.08663829787234\t1.32242888402626\t0.9820310805927\t1.04469323779669\n-1203\t1.10574636879399\t0.91761198121937\t1.07498986623429\t0.954758190327613\t0.902372322899506\t1.05106382978723\t1.17525984682713\t1.05059631369715\t1.11240483654277\n-1204\t1.06972857176487\t0.959559957503684\t1.0088366436968\t1.01262232307474\t0.972948929159802\t1.02127659574468\t1.20315919037199\t0.972262378026744\t1.04388714733542\n-1205\t0.994091198003719\t0.970046951574763\t1.02537494933117\t0.954758190327613\t0.983031301482702\t1.08936170212766\t1.08807439824945\t0.976870256595591\t0.931034482758621\n-1206\t0.886037806916359\t0.970046951574763\t0.955087150385083\t0.972840731811091\t0.947742998352554\t0.94468085106383\t1.05320021881838\t1.00912540657752\t0.959247648902821\n-1207\t1.05171967325031\t0.933342472325988\t1.01297122010539\t0.93305914054744\t0.917495881383855\t0.982978723404255\t1.00786378555799\t0.972262378026744\t0.983430362740708\n-1208\t1.00489653711246\t0.959559957503684\t1.04604783137414\t0.994539781591264\t1.00823723228995\t1.01276595744681\t1.05668763676149\t0.999909649439827\t0.991491267353336\n-1209\t1.34346382918619\t1.15356934781864\t1.26518038102959\t1.31640901999716\t1.0737726523888\t1.20425531914894\t1.19269693654267\t1.23951933501988\t1.12449619346171\n-1210\t1.2413173568116\t1.11749408821413\t1.25029590595865\t1.25333711530279\t1.12277298187809\t1.0743829787234\t1.08472647702407\t1.13685580050596\t1.07564711150918\n-1211\t1.12375526730855\t0.98577744268138\t1.09152817186867\t1.05240391433839\t0.967907742998353\t1.07659574468085\t0.997401531728665\t1.07824358511023\t1.07613076578594\n-1212\t1.05892323265614\t1.04869940710785\t0.979894608836644\t1.00900581477805\t0.993113673805601\t1\t0.979964442013129\t1.04138055655945\t1.06806986117331\n-1213\t0.990489418300808\t0.996264436752459\t1.0088366436968\t1.03432137285491\t1.01831960461285\t0.987234042553191\t0.986939277899344\t1.02294904228406\t1.08419167039857\n-1214\t1.07333035146778\t0.875664004935056\t1.06258613700851\t1.05240391433839\t0.967907742998353\t1.02127659574468\t1.0601750547046\t1.02294904228406\t1.08822212270488\n-1215\t1.15256950493185\t0.964803454539223\t1.11633563032023\t1.07048645582187\t1.0939373970346\t1.17021276595745\t1.13689824945295\t1.08745934224792\t1.205105239588\n-1216\t1.05532145295322\t0.98577744268138\t1.12873935954601\t1.02708835626152\t1.0031960461285\t1.08936170212766\t1.13341083150985\t1.04138055655945\t1.08419167039857\n-1217\t0.950869841568775\t0.975290448610302\t0.959221726793677\t0.961991206921004\t1.02840197693575\t0.970212765957447\t0.955552516411379\t0.972262378026744\t1.01970443349754\n-1218\t0.943666282162951\t0.970046951574763\t0.959221726793677\t0.9656077152177\t0.932619439868204\t0.906382978723404\t0.927653172866521\t1.05981207083484\t1.00761307657859\n-1219\t0.860825348995975\t0.933342472325988\t0.984029185245237\t0.969224223514395\t0.927578253706755\t0.957446808510638\t0.892778993435449\t0.944615106613661\t0.96730855351545\n-1220\t0.929259163351303\t0.938585969361527\t1.00056749087961\t0.889661040987094\t0.962866556836903\t1.00425531914894\t1.07761214442013\t0.986086013733285\t1.08016121809225\n-1221\t0.997692977706632\t0.975290448610302\t0.971625456019457\t0.940292157140831\t0.942701812191104\t1.0936170212766\t1.27290754923414\t1.08745934224792\t1.12449619346171\n-1222\t0.983285858894983\t0.975290448610302\t0.946817997567896\t0.918593107360658\t0.942701812191104\t1.05106382978723\t1.13689824945295\t1.0459884351283\t1.0237348858038'..b'1.02198251523589\n-1333\t1.07113796382253\t1.17089568584911\t1.04407042526568\t1.14721932750828\t1.0625943700308\t1.06123959296947\t1.05168395014746\t1.06261686648544\t1.026188204599\n-1334\t1.0297957967978\t1.08335208316881\t0.923268888458081\t1.08683936290258\t0.98894921567223\t0.981313598519889\t1.03712777090667\t1.0001099919863\t0.950485796063007\n-1335\t0.988453629773075\t0.957508154315864\t0.931897569658624\t0.913246964661195\t0.941605902156006\t0.945790934320074\t0.887926933688517\t0.995301770870979\t0.946280106699897\n-1336\t0.871943886339746\t0.935622253645788\t0.811096032851025\t0.886830730146202\t0.925824797650598\t0.941350601295097\t0.902483112929312\t0.971260665294386\t0.963102864152339\n-1337\t0.860668749878457\t0.979394054985941\t0.836982076452653\t0.943436946964045\t0.978428479335291\t0.914708603145236\t0.851536485586528\t0.937603117487155\t0.90001752370568\n-1338\t0.884073199805679\t1.08111375241846\t0.81188045841471\t0.883743118319774\t0.940410363935899\t0.923791102514507\t0.88643823353889\t0.929953674803693\t1.00248341000692\n-1339\t0.856910371058027\t0.946565203980826\t0.862868120054282\t0.924568208024764\t0.952126638492945\t0.945790934320074\t0.884287888878318\t0.952027780833111\t0.971514242878561\n-1340\t0.920802811005336\t0.935622253645788\t0.793838670449939\t0.909473216873339\t0.994209583840699\t0.959111933395005\t0.906122157739511\t0.865479800757373\t0.992542689694114\n-1341\t0.856910371058027\t0.968451104650903\t0.94915493205971\t0.901925721297627\t0.946866270324475\t0.892506938020352\t0.924317381790505\t0.91837023302588\t0.958897174789229\n-1342\t0.958386599209635\t0.913736352975711\t0.923268888458081\t0.966079433691182\t0.994209583840699\t0.892506938020352\t0.9388735610313\t0.961644223063748\t0.971514242878561\n-1343\t0.856910371058027\t0.962979629483384\t0.893068504256182\t0.939663199176188\t0.973168111166822\t0.932469935245143\t0.866092664827324\t0.923178454141198\t0.984131310967893\n-1344\t0.950869841568775\t0.99033700532098\t0.91895454785781\t0.958531938115469\t0.983688847503761\t0.892506938020352\t0.942512605841499\t0.889520906333967\t0.96730855351545\n-1345\t0.884073199805679\t0.966710180733965\t0.888558057264989\t0.919250654323694\t1.0009045978733\t0.974854932301741\t0.939700616669982\t0.919900121562572\t0.940927411146847\n-1346\t0.879460643980606\t0.946565203980826\t0.94915493205971\t0.920794460236907\t1.00999068834611\t0.905827937095282\t0.913400247359909\t0.985685328640342\t0.929457349247454\n-1347\t0.920802811005336\t0.935622253645788\t0.88875416365591\t0.943436946964045\t0.925824797650598\t0.910268270120259\t0.924317381790505\t0.971260665294386\t0.874783387527016\n-1348\t1.10120499438597\t1.00675143082354\t1.07858515006785\t1.10948184962972\t1.06785473819927\t1.16336725254394\t1.20452383217582\t1.06742508760076\t1.11030199186121\n-1349\t1.10120499438597\t0.984865530153461\t1.10015685306921\t1.10570810184186\t1.08889621087315\t1.06567992599445\t1.17177242888403\t1.13954840433054\t1.13974181740299\n-1350\t1.05610444854081\t1.01769438115858\t0.996612678662695\t0.973626929266894\t0.946866270324475\t0.967992599444958\t1.05532299495766\t1.0770415298314\t1.00936544714656\n-1351\t0.935152984683341\t1.00103125223931\t0.996808785053617\t0.907414808989054\t0.989905646248315\t0.960928433268859\t0.989158543863139\t1.02546243059434\t0.905752554655376\n-1352\t0.898252538082756\t0.962979629483384\t0.975040975661338\t0.947210694751901\t0.994209583840699\t0.910268270120259\t0.862453620017125\t0.956836001948429\t0.870577698163905\n-1353\t0.890735780441896\t0.957508154315864\t0.923268888458081\t0.962305685903325\t0.931085165819067\t0.874745605920444\t0.913400247359909\t0.947219559717792\t0.887400455616348\n-1354\t1.06362120618167\t1.11618093417392\t1.04838476586595\t1.07551811953901\t1.02051142468305\t1.08344125809436\t1.09535248786985\t1.11069907763863\t1.07245078759322\n-1355\t1.17876426640757\t1.01819178799199\t1.08701772487747\t1.1007336161215\t1.0558993559982\t1.09555125725338\t1.09948776606326\t1.05059631369714\t1.03765826649839\n-1356\t1.25341933661339\t1.11461765555463\t1.12696739822804\t1.128350588569\t1.02840197693575\t1.09422492401216\t1.08807439824945\t1.10589085652331\t0.953489859893801\n-1357\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\n' |
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| Binary file test-data/preprocessing_results5.RData has changed |
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| diff -r ae9ffc7ba261 -r d4803c1e5e19 test-data/preprocessing_results5.pdf |
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| diff -r ae9ffc7ba261 -r d4803c1e5e19 test-data/preprocessing_results5.txt --- a/test-data/preprocessing_results5.txt Thu Oct 25 07:28:42 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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 -301 0 0 0 0 0 0 0 0 0 -302 0 4.32197925754431e-23 0 0 0 0 0 0 0 -303 0 1.28620729883923e-30 0 0.00308917369693518 0 0 0 0 0 -304 0 1.32924944261294e-38 0 2.8316210487489e-10 0.411686420440674 0 0 0 0.609295308589935 -305 0 0 0 5.69736818276873e-18 0 0 0.716848015785217 0 0 -306 0 0.180751591920853 0.0924000516533852 3.22355374818131e-26 0.228940084576607 0 0 0 0.338278532028198 -307 5.31794802036641e-23 1.36712752230039e-09 0 0.503042221069336 0.171210870146751 0 0 0.0994685217738152 0.00513129541650414 -308 1.42257959582276e-30 0 0 0 0 0 0 0.0315862037241459 0.322940319776535 -309 1.43981749664202e-38 2.37613022591177e-07 0 0 1.4921518187716e-10 0 7.17280070103395e-32 1.14764100445086e-08 0 -310 0 2.2688041766486e-14 0.0299898684024811 0 4.55189177922775e-18 0 0 2.89623705606364e-14 0 -311 0 4.60080996999485e-22 9.34697319543432e-10 3.53486932303922e-32 5.44664266518465e-26 0 0 6.9618325415624e-22 0 -312 0 0 1.14256191537071e-17 0 0 0 0 6.04272858040201e-30 1.25046502952903e-32 -313 0 0 0 0 0 0 0 0.000948468048591167 0 -314 0 0.343302994966507 0 0 0 0 0 0 0 -315 0 0 0.12950636446476 0 0 0 0 0 0 -316 0.327463179826736 0 1.93941795956221e-09 0.00699668889865279 0 0 0 0.0240590367466211 0 -317 1.18278642435854e-09 0 0 1.591814253743e-07 0 0 0 7.10978553808417e-10 0 -318 0 2.88274619950529e-32 0.312686443328857 1.89643697338752e-14 0 0 0 8.22819137337219e-18 0 -319 0 0 3.68662113032769e-05 3.99332497384422e-22 0 0 0 0 0 -320 0 0 5.68011697044319e-15 2.58921175367487e-30 0 0 0 0 0 -321 0 0 0 0 0 0 0.0821415111422539 0 0 -322 0 0 0 0 0 0 1.23654897432601e-09 8.91581066753133e-07 0 -323 0 0 0 0 0 0 0 3.62019611608189e-14 0 -324 0 0 0 0 0 0 1.41676795295531e-10 5.43261166662179e-22 0 -325 0 0 0 0 0 0 3.87320208074687e-18 0 0 -326 0 0 0 0 0 0 4.08673089735238e-26 0 0.0913732051849365 -327 0.0852032229304314 0 0 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7.14956786396215e-06 0 0 0 2.40733255552072e-09 0 0 -337 0 0 9.22569177086094e-14 0 0 1.92654253432319e-23 0.129606500267982 0 0 -338 0 0 0 0 0 8.21688042580719e-31 0 0 0 -339 0 0 0 0 0 1.2691101966792e-38 0 0 0 -340 0 0 0 0 0.131738051772118 0 0 0 0 -341 0 0 0 0 1.97074911945094e-09 0 2.68033400688056e-31 0 0 -342 0 0 0 0 0 0 0 0 0 -343 0 0.540803730487823 0 0.311067968606949 0 0 0.456998586654663 0 1.1592504051805e-05 -344 0 0.760098695755005 0 1.23029351234436 0.179359897971153 0 0 0 0.385462760925293 -345 1.29758274555206 1.30673027038574 0.626297771930695 0.370624721050262 0.266427725553513 0.95829576253891 0.664171636104584 0.340830773115158 0.920338690280914 -346 0 1.22390151023865 0 0.25139981508255 0 0.280698895454407 0 0 0.700047612190247 -347 0 0.0356887876987457 0 0.208728492259979 0 0 0 0.0668430551886559 0 -348 0 9.81050796156069e-10 5.19627293105376e-24 2.63146238133061e-09 0 0 9.31592096266419e-23 1.41976275180866e-09 0 -349 0 1.04223425420895e-17 6.50702138942878e-31 0 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