| Previous changeset 1:aac805a9d2ae (2018-10-25) Next changeset 3:4b5513e25902 (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:
filtering.xml macros.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 aac805a9d2ae -r 0c4579390f73 filtering.xml --- a/filtering.xml Thu Oct 25 07:25:13 2018 -0400 +++ b/filtering.xml Fri Feb 15 10:15:15 2019 -0500 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.1">\n+<tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.2">\n <description>tool for filtering mass spectrometry imaging data</description>\n <macros>\n <import>macros.xml</import>\n@@ -15,16 +15,13 @@\n cat \'${MSI_subsetting}\' &&\n Rscript \'${MSI_subsetting}\' &&\n \n- #if $imzml_output:\n+ #if str($imzml_output) == "imzml_format":\n mkdir $outfile_imzml.files_path &&\n- ls -l &&\n mv ./out.imzML "${os.path.join($outfile_imzml.files_path, \'imzml\')}" | true &&\n mv ./out.ibd "${os.path.join($outfile_imzml.files_path, \'ibd\')}" | true &&\n #end if\n echo "imzML file:" > $outfile_imzml &&\n ls -l "$outfile_imzml.files_path" >> $outfile_imzml\n-\n-\n ]]>\n </command>\n \n@@ -58,30 +55,13 @@\n ## Range y coordinates\n minimumy = min(coord(msidata)[,2])\n maximumy = max(coord(msidata)[,2])\n- ## Number of intensities > 0\n- npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)\n- ## Spectra multiplied with m/z (potential number of peaks)\n- numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])\n- ## Percentage of intensities > 0\n- percpeaks = round(npeaks/numpeaks*100, digits=2)\n- ## Number of empty TICs\n- TICs = colSums(spectra(msidata)[], na.rm=TRUE) \n- NumemptyTIC = sum(TICs == 0)\n- ## median TIC\n- medint = round(median(TICs), digits=2)\n ## Store features for QC plot\n featuresinfile = mz(msidata)\n \n-## Next steps will only run if there are more than 0 intensities/pixels/features in the file\n-\n-if (sum(spectra(msidata)[]>0, na.rm=TRUE) > 0)\n-{\n+## Next steps will only run if there are more than 0 pixels/features in the file\n \n-\n- ## prepare dataframe for QC of pixel distribution (will be overwritten in filtering of pixels condition)\n- position_df = cbind(coord(msidata)[,1:2], rep("$infile.element_identifier", times=ncol(msidata)))\n- colnames(position_df)[3] = "annotation"\n-\n+if (ncol(msidata)>0 & nrow(msidata) >0)\n+{\n ###################################### Filtering of pixels #####################\n ################################################################################\n \n@@ -93,69 +73,90 @@\n ## read tabular file\n input_list = read.delim("$pixels_cond.annotation_file", header = $pixels_cond.tabular_header, \n stringsAsFactors = FALSE)\n- numberpixels = nrow(input_list)\n- inputpixels = input_list[,c($pixels_cond.column_x, $pixels_cond.column_y, $pixels_cond.column_names)]\n+ inputpixels = input_list[,c($pixels_cond.column_x, $pixels_cond.column_y)]\n+ input_pixels = paste(inputpixels[,1], inputpixels[,2], sep="_")\n+ dataset_pixels = paste(coord(msidata)\\$x, coord(msidata)\\$y, sep="_")\n+ pixelsofinterest = dataset_pixels %in% input_pixels\n \n- ## rewrite into x = 1, y = 1 format and filter msidata, count validpixels\n- pixelvector = character()\n- for (pixel in 1:nrow(inputpixels)){\n- pixelvector[pixel] = paste0("x = ", inputpixels[pixel,1],", ", "y = ", inputpixels[pixel,2])}\n- pixelsofinterest= pixels(msidata)[names(pixels(msidata)) %in% pixelvector]\n- msidata = msidata[,pixelsofinterest]\n+ tryCatch(\n+ {\n+ msidata = msidata[,pixelsofinterest]\n+ if (ncol(msidata) == 0)\n+ {\n+ stop(call.=FALSE)\n+ }\n+ },\n+ error=function(cond) {\n+ ## in case all coordinates were outside the dataset leading to zero pixels, tool is stopped to avoid continuing with wrong data\n+ message("Error during pixel filtering")\n+ message("Possible problems: Forgot to set \'Tabular file contains a header line\' = Yes, wrong column'..b' \n+ 2 1 \n+ 3 1 \n+ ...\n+ ...\n \n @MZ_TABULAR_INPUT_DESCRIPTION@\n \n **Options**\n \n-- pixel filtering/annotation: either with a tabular file containing x and y coordinates and pixel annotations or by defining a range for x and y by hand (for the latter no annotation is possible). Pixel that are not present in the dataset are ignored. It is not possible to filter only for pixels that are not present in the dataset. \n-- m/z feature filtering: m/z values for filtering should be either imported as a tabular file containing containing m/z of interest or by defining a range for the m/z values. m/z that are not present in the dataset are ignored. It is not possible to filter only for m/z that are not present in the dataset. \n-- m/z feature removing: perturbing m/z features such as matrix contaminants can be removed by specifying their m/z in a tabular file, optionally with a half window size in ppm or m/z for the window in which peaks should be removed.\n+- Pixel filtering/annotation: \n+\n+ - Either with a tabular file containing x and y coordinates or by entering x-min, x-max, y-min, y-max manually\n+ - Pixel that are not present in the dataset are ignored\n+ - An error occurs if the input for filtering (tabular file, x-range or y-range) contains not a single coordinate that occurs in the input dataset\n+\n+\n+- m/z feature filtering: \n+\n+ - Either with a tabular file containing m/z values or by entering m/z-min and m/z-max manually\n+ - m/z values that are not present in the dataset are ignored\n+ - An error occurs if the input for filtering (tabular file or mz-range) contains not a single m/z feature that occurs in the dataset\n+\n+\n+- m/z feature removing: \n+\n+ - Perturbing m/z features such as matrix contaminants can be removed by specifying their m/z value in a tabular file, optionally with a half window size in ppm or m/z for the window in which peaks should be removed\n \n \n **Tips**\n \n-- Numeric m/z features imported via a tabular file and m/z features of the dataset are rounded to 4 decimal points (or maximum number of decimal points of input m/z) and then matched. Therefore, it is recommended to use the filtering tool only for m/z which have been extracted from the same dataset. If the m/z values are from a different dataset, the tool "Join two files on column allowing a small difference" should be used to find corresponding m/z values, which can then be used for filtering. \n-- In case tabular file cannot be selected in drop-down menu: Datatype in Galaxy must be tabular otherwise file will not appear in selection window (if Galaxy auto-detection was wrong, datatype can be changed by pressing the pen button (edit attributes))\n+- m/z feautre filtering with a tabular file: \n+\n+ - For matching the m/z features of the input dataset are rounded to the number of decimal points of the m/z values from the tabular file. In case the input had more than 4 digits m/z values of dataset and tabular file are rounded to 4 digits. \n+ - Therefore, it is recommended to use the filtering tool only for m/z features which have been extracted from the same dataset. If the m/z values are from a different dataset, the tool \'Join two files on column allowing a small difference\' should be used to find corresponding m/z values, which can then be used for filtering. \n+\n+- Problems to select tabular file: \n+\n+ - In case tabular file cannot be selected in drop-down menu: Datatype in Galaxy might be different from \'tabular\' - datatype can be changed by pressing the pen button of the dataset (edit attributes)\n \n \n **Output**\n \n-- MSI data as .RData output (can be read with the Cardinal package in R)\n-- optional: MSI data as imzML file\n+- MSI data as imzML file or .RData (can be read with the Cardinal package in R)\n - pdf with heatmap showing the pixels that are left after filtering and histograms of kept and removed m/z\n \n \n' |
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| diff -r aac805a9d2ae -r 0c4579390f73 macros.xml --- a/macros.xml Thu Oct 25 07:25:13 2018 -0400 +++ b/macros.xml Fri Feb 15 10:15:15 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 aac805a9d2ae -r 0c4579390f73 test-data/112_auto_combined.RData |
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| diff -r aac805a9d2ae -r 0c4579390f73 test-data/112_auto_combined.ibd |
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| diff -r aac805a9d2ae -r 0c4579390f73 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 10:15:15 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 aac805a9d2ae -r 0c4579390f73 test-data/features_test4.tabular --- a/test-data/features_test4.tabular Thu Oct 25 07:25:13 2018 -0400 +++ b/test-data/features_test4.tabular Fri Feb 15 10:15:15 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 aac805a9d2ae -r 0c4579390f73 test-data/features_test6.tabular --- a/test-data/features_test6.tabular Thu Oct 25 07:25:13 2018 -0400 +++ b/test-data/features_test6.tabular Fri Feb 15 10:15:15 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 aac805a9d2ae -r 0c4579390f73 test-data/features_test7.tabular --- a/test-data/features_test7.tabular Thu Oct 25 07:25:13 2018 -0400 +++ b/test-data/features_test7.tabular Fri Feb 15 10:15:15 2019 -0500 |
| b |
| b'@@ -1,101 +1,101 @@\n 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| diff -r aac805a9d2ae -r 0c4579390f73 test-data/loadings_pca.tabular --- a/test-data/loadings_pca.tabular Thu Oct 25 07:25:13 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r aac805a9d2ae -r 0c4579390f73 test-data/out3.ibd |
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| Binary file test-data/out3.ibd has changed |
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| diff -r aac805a9d2ae -r 0c4579390f73 test-data/out3.imzml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out3.imzml Fri Feb 15 10:15:15 2019 -0500 |
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| diff -r aac805a9d2ae -r 0c4579390f73 test-data/out3.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out3.imzml.txt Fri Feb 15 10:15:15 2019 -0500 |
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| diff -r aac805a9d2ae -r 0c4579390f73 test-data/out4.imzml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out4.imzml Fri Feb 15 10:15:15 2019 -0500 |
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| diff -r aac805a9d2ae -r 0c4579390f73 test-data/out4.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out4.imzml.txt Fri Feb 15 10:15:15 2019 -0500 |
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| diff -r aac805a9d2ae -r 0c4579390f73 test-data/out5.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out5.imzml.txt Fri Feb 15 10:15:15 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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| diff -r aac805a9d2ae -r 0c4579390f73 test-data/out6.imzml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out6.imzml Fri Feb 15 10:15:15 2019 -0500 |
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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 aac805a9d2ae -r 0c4579390f73 test-data/preprocessing_results4.txt --- a/test-data/preprocessing_results4.txt Thu Oct 25 07:25:13 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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| diff -r aac805a9d2ae -r 0c4579390f73 test-data/preprocessing_results5.RData |
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| diff -r aac805a9d2ae -r 0c4579390f73 test-data/preprocessing_results5.pdf |
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| diff -r aac805a9d2ae -r 0c4579390f73 test-data/preprocessing_results5.txt --- a/test-data/preprocessing_results5.txt Thu Oct 25 07:25:13 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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