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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d |
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modified:
data_exporter.xml macros.xml test-data/Example_Processed.imzML test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf test-data/features_test2.tabular test-data/features_test4.tabular test-data/features_test6.tabular test-data/features_test7.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:
static/images/classification_overview.png |
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| diff -r d94770c22f13 -r e521b5767819 data_exporter.xml --- a/data_exporter.xml Thu Feb 28 09:24:07 2019 -0500 +++ b/data_exporter.xml Fri Mar 22 08:16:20 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="cardinal_data_exporter" name="MSI data exporter" version="@VERSION@.1"> +<tool id="cardinal_data_exporter" name="MSI data exporter" version="@VERSION@.2"> <description> exports imzML and Analyze7.5 to tabular files </description> @@ -24,8 +24,6 @@ @READING_MSIDATA_INRAM@ -## to make sure that processed files work as well: -iData(msidata) = iData(msidata)[] ###################### Intensity matrix output ################################ @@ -37,12 +35,11 @@ pixel_names = gsub(", y = ", "_", names(pixels(msidata))) pixel_names = gsub(" = ", "y_", pixel_names) - spectramatrix = cbind(mz_names,spectra(msidata)[]) - newmatrix = rbind(c("mz_name", pixel_names), spectramatrix) + ##spectramatrix = cbind(mz_names,spectra(msidata)) + newmatrix = rbind(c("mz_name", pixel_names), cbind(mz_names,spectra(msidata))) write.table(newmatrix, file="$intensity_matrix", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t") ## free up RAM space in case furhter steps will be run: rm(newmatrix) - rm(spectramatrix) gc() #end if @@ -56,19 +53,22 @@ mz_names = gsub("/", "", mz_names) ## mean, median, sd and SEM intensity per file and mz - full_sample_mean = apply(spectra(msidata)[],1,mean, na.rm=TRUE) - full_sample_median = apply(spectra(msidata)[],1,median, na.rm=TRUE) - full_sample_sd = apply(spectra(msidata)[],1,sd, na.rm=TRUE) + full_sample_mean = rowMeans(spectra(msidata), na.rm=TRUE) + full_sample_median = apply(spectra(msidata),1,median, na.rm=TRUE) + full_sample_sd = apply(spectra(msidata),1,sd, na.rm=TRUE) full_sample_sem = full_sample_sd/full_sample_mean*100 ## npeaks and sum of all intensities per spectrum and mz - npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE) - mzTIC = rowSums(spectra(msidata)[], na.rm=TRUE) ## calculate intensity sum for each m/z - peakspermz = rowSums(spectra(msidata)[] > 0, na.rm=TRUE) ## calculate number of intensities > 0 for each m/z (max = number of spectra) + npeaks= sum(spectra(msidata)>0, na.rm=TRUE) + mzTIC = rowSums(spectra(msidata), na.rm=TRUE) ## calculate intensity sum for each m/z + peakspermz = rowSums(spectra(msidata) > 0, na.rm=TRUE) ## calculate number of intensities > 0 for each m/z (max = number of spectra) ## combine into dataframe, order is the same for all vectors mz_df = data.frame(mz_names, mz(msidata), full_sample_mean, full_sample_median, full_sample_sd, full_sample_sem, mzTIC, peakspermz) colnames(mz_df) = c("mz_names", "mz", "sample_mean", "sample_median", "sample_sd", "sample_sem", "intensity_sum", "number_peaks") write.table(mz_df, file="$feature_output", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") + ## free up RAM space in case furhter steps will be run: + rm(mz_df) + gc() #end if ###################### summarized m/z feature output ####################### @@ -101,7 +101,7 @@ count = 1 for (subsample in levels(msidata\$annotation)){ subsample_pixels = msidata[,msidata\$annotation == subsample] - subsample_calc = apply(spectra(subsample_pixels)[],1,mean, na.rm=TRUE) + subsample_calc = rowMeans(spectra(subsample_pixels), na.rm=TRUE) sample_matrix = cbind(sample_matrix, subsample_calc) count = count+1} sample_matrix_mean = cbind(mz_names,sample_matrix) @@ -116,7 +116,7 @@ count = 1 for (subsample in levels(msidata\$annotation)){ subsample_pixels = msidata[,msidata\$annotation == subsample] - subsample_calc = apply(spectra(subsample_pixels)[],1,median, na.rm=TRUE) + subsample_calc = apply(spectra(subsample_pixels),1,median, na.rm=TRUE) sample_matrix = cbind(sample_matrix, subsample_calc) count = count+1} sample_matrix_median = cbind(mz_names,sample_matrix) @@ -131,7 +131,7 @@ count = 1 for (subsample in levels(msidata\$annotation)){ subsample_pixels = msidata[,msidata\$annotation == subsample] - subsample_calc = apply(spectra(subsample_pixels)[],1,sd, na.rm=TRUE) + subsample_calc = apply(spectra(subsample_pixels),1,sd, na.rm=TRUE) sample_matrix = cbind(sample_matrix, subsample_calc) count = count+1} sample_matrix_sd = cbind(mz_names,sample_matrix) @@ -156,19 +156,19 @@ pixelxyarray=1:length(pixels(msidata)) ## number of pixels per spectrum: every intensity value > 0 counts as peak - peaksperpixel = apply(spectra(msidata)[]> 0, 2, sum, na.rm=TRUE) + peaksperpixel = colSums(spectra(msidata)>0, na.rm=TRUE) ## Total ion chromatogram per spectrum - TICs = round(apply(spectra(msidata)[],2, sum, na.rm=TRUE), digits = 2) + TICs = round(colSums(spectra(msidata), na.rm=TRUE), digits = 2) ## Median ion intensity per spectrum - med_int = round(apply(spectra(msidata)[], 2, median, na.rm=TRUE), digits = 2) + med_int = round(apply(spectra(msidata), 2, median, na.rm=TRUE), digits = 2) ## Maximum ion intensity per spectrum - max_int = round(apply(spectra(msidata)[], 2, max, na.rm=TRUE), digits = 2) + max_int = round(apply(spectra(msidata), 2, max, na.rm=TRUE), digits = 2) ## Highest m/z per spectrum - highestmz = apply(spectra(msidata)[],2,which.max) + highestmz = apply(spectra(msidata),2,which.max) highestmz_data = mz(msidata)[highestmz] ## Combine into dataframe; order is the same for all vectors @@ -197,13 +197,13 @@ for (mass in 1:length(inputcalibrantmasses)){ filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],] - if (nrow(filtered_data) > 1 & sum(spectra(filtered_data)[],na.rm=TRUE) > 0){ + if (nrow(filtered_data) > 1 & sum(spectra(filtered_data),na.rm=TRUE) > 0){ ## intensity of all m/z > 0 - intensity_sum = apply(spectra(filtered_data)[],2,sum, na.rm=TRUE) > 0 + intensity_sum = colSums(spectra(filtered_data), na.rm=TRUE) > 0 - }else if(nrow(filtered_data) == 1 & sum(spectra(filtered_data)[], na.rm=TRUE) > 0){ + }else if(nrow(filtered_data) == 1 & sum(spectra(filtered_data), na.rm=TRUE) > 0){ ## intensity of only m/z > 0 - intensity_sum = spectra(filtered_data)[] > 0 + intensity_sum = spectra(filtered_data) > 0 }else{ intensity_sum = rep(FALSE, ncol(filtered_data))} ## for each pixel add sum of intensities > 0 in the given m/z range |
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| diff -r d94770c22f13 -r e521b5767819 macros.xml --- a/macros.xml Thu Feb 28 09:24:07 2019 -0500 +++ b/macros.xml Fri Mar 22 08:16:20 2019 -0400 |
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| @@ -99,6 +99,7 @@ #if str($processed_cond.processed_file) == "processed": msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units") centroided(msidata) = $centroids + iData(msidata) = iData(msidata)[] #else msidata <- readImzML('infile') centroided(msidata) = $centroids @@ -129,14 +130,16 @@ 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) + 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) + 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 - NAcount = sum(is.na(spectra(msidata)[])) - ## Number of NA in spectra matrix - infcount = sum(is.infinite(spectra(msidata)[])) + infcount = sum(is.infinite(spectra(msidata))) + ## Number of duplicated coordinates + dupl_coord = sum(duplicated(coord(msidata))) properties = c("Number of m/z features", "Range of m/z values", @@ -145,7 +148,8 @@ "Range of y coordinates", "Range of intensities", "Number of NA intensities", - "Number of Inf intensities") + "Number of Inf intensities", + "Number of duplicated coordinates") values = c(paste0(maxfeatures), paste0(minmz, " - ", maxmz), @@ -154,7 +158,8 @@ paste0(minimumy, " - ", maximumy), paste0(minint, " - ", maxint), paste0(NAcount), - paste0(infcount)) + paste0(infcount), + paste0(dupl_coord)) property_df = data.frame(properties, values) ]]></token> @@ -229,7 +234,7 @@ <xml name="reading_msidata"> <param name="infile" type="data" format="imzml,rdata,analyze75" label="MSI data" - help="Input file as imzML (composite upload), or Cardinal MSImageSet saved as RData (regular upload)"/> + help="Input file as imzML (composite upload), Analyze7.5 (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"> |
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| diff -r d94770c22f13 -r e521b5767819 static/images/classification_overview.png |
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| diff -r d94770c22f13 -r e521b5767819 test-data/Example_Processed.imzML --- a/test-data/Example_Processed.imzML Thu Feb 28 09:24:07 2019 -0500 +++ b/test-data/Example_Processed.imzML Fri Mar 22 08:16:20 2019 -0400 |
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| b'@@ -1,373 +1,380 @@\n-<?xml version="1.0" encoding="ISO-8859-1"?>\r\n-<mzML 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" version="1.1">\r\n- <cvList count="3">\r\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo"/>\r\n- <cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\r\n- <cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo"/>\r\n- </cvList>\r\n- <fileDescription>\r\n- <fileContent>\r\n- <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>\r\n- <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value=""/>\r\n- <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{9D501BDC-5344-4916-B7E9-7E795B02C856}"/>\r\n- <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7E8FDB93053915D3EDB51B70AA0619AC209964DF"/>\r\n- <cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value=""/>\r\n- </fileContent>\r\n- <sourceFileList count="1">\r\n- <sourceFile id="sf1" name="Example.raw" location="C:\\Users\\Thorsten Schramm\\Documents\\Promotion\\imzML\\Website\\files\\Beispiel-Dateien\\Example images\\">\r\n- <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW file" value=""/>\r\n- <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>\r\n- <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7623BE263B25FF99FDF017154B86FAB742D4BB0B"/>\r\n- </sourceFile>\r\n- </sourceFileList>\r\n- <contact>\r\n- <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Thorsten Schramm"/>\r\n- <cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value="Institut f\xfcr Anorganische und Analytische Chemie"/>\r\n- <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Schubertstra\xdfe 60, Haus 16, Gie\xdfen, Germany"/>\r\n- <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="thorsten.schramm@anorg.chemie.uni-.giessen.de"/>\r\n- </contact>\r\n- </fileDescription>\r\n- <referenceableParamGroupList count="4">\r\n- <referenceableParamGroup id="mzArray">\r\n- <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>\r\n- <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>\r\n- <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>\r\n- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>\r\n- </referenceableParamGroup>\r\n- <referenceableParamGroup id="intensityArray">\r\n- <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>\r\n- <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>\r\n- <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>\r\n- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>\r\n- </referenceableParamGroup>\r\n- <referenceableParamGroup id="scan1">\r\n- <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value=""/>\r\n- <cvParam cvRef="MS" accession="MS:1000095" name="linear" value=""/>\r\n- <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS - p NSI Full ms [100,00-800,00]"/>\r\n- </referenceableParamGroup>\r\n- <referenceableParamGroup id="spectrum1">\r\n- <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>\r\n- <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>\r\n- <cvParam cvRef="MS" accession'..b' <referenceableParamGroupRef ref="intensityArray"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="436764"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>\n+ <binary />\n+ </binaryDataArray>\n+ </binaryDataArrayList>\n+ </spectrum>\n+ <spectrum id="Scan=8" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="7">\n+ <referenceableParamGroupRef ref="spectrum1"/>\n+ <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="168.27018147522492"/>\n+ <scanList count="1">\n+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>\n+ <scan instrumentConfigurationRef="LTQFTUltra0">\n+ <referenceableParamGroupRef ref="scan1"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>\n+ </scan>\n+ </scanList>\n+ <binaryDataArrayList count="2">\n+ <binaryDataArray encodedLength="0">\n+ <referenceableParamGroupRef ref="mzArray"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="470360"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>\n+ <binary />\n+ </binaryDataArray>\n+ <binaryDataArray encodedLength="0">\n+ <referenceableParamGroupRef ref="intensityArray"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="503956"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>\n+ <binary />\n+ </binaryDataArray>\n+ </binaryDataArrayList>\n+ </spectrum>\n+ <spectrum id="Scan=9" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="8">\n+ <referenceableParamGroupRef ref="spectrum1"/>\n+ <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="243.5395066031077"/>\n+ <scanList count="1">\n+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>\n+ <scan instrumentConfigurationRef="LTQFTUltra0">\n+ <referenceableParamGroupRef ref="scan1"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>\n+ </scan>\n+ </scanList>\n+ <binaryDataArrayList count="2">\n+ <binaryDataArray encodedLength="0">\n+ <referenceableParamGroupRef ref="mzArray"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="537552"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>\n+ <binary />\n+ </binaryDataArray>\n+ <binaryDataArray encodedLength="0">\n+ <referenceableParamGroupRef ref="intensityArray"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="571148"/>\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>\n+ <binary />\n+ </binaryDataArray>\n+ </binaryDataArrayList>\n+ </spectrum>\n+ </spectrumList>\n+ </run>\n+</mzML>\n' |
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| diff -r d94770c22f13 -r e521b5767819 test-data/features_test2.tabular --- a/test-data/features_test2.tabular Thu Feb 28 09:24:07 2019 -0500 +++ b/test-data/features_test2.tabular Fri Mar 22 08:16:20 2019 -0400 |
| b |
| b'@@ -99,3 +99,8057 @@\n 946.450012207031\t2\tA\t0.003494\t0.042887\t0.032578\n 979.395385742188\t2\tC\t0.003494\t-0.009858\t-0.008482\n 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|
| b |
| diff -r d94770c22f13 -r e521b5767819 test-data/features_test4.tabular --- a/test-data/features_test4.tabular Thu Feb 28 09:24:07 2019 -0500 +++ b/test-data/features_test4.tabular Fri Mar 22 08:16:20 2019 -0400 |
| b |
| b'@@ -99,3 +99,8057 @@\n 927.295166015625\t3\tA\t0.00081\t0.03242\t0.019578\n 957.467712402344\t3\tA\t0.000805\t0.034961\t0.029421\n 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|
| b |
| diff -r d94770c22f13 -r e521b5767819 test-data/features_test6.tabular --- a/test-data/features_test6.tabular Thu Feb 28 09:24:07 2019 -0500 +++ b/test-data/features_test6.tabular Fri Mar 22 08:16:20 2019 -0400 |
| b |
| b'@@ -19,3 +19,8137 @@\n 900.434692382812\t2\t3\t2\tA\t30.041667\t0\t1\t1\n 900.470520019531\t2\t3\t2\tA\t19.166667\t0\t1\t1\n 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|
| b |
| diff -r d94770c22f13 -r e521b5767819 test-data/features_test7.tabular --- a/test-data/features_test7.tabular Thu Feb 28 09:24:07 2019 -0500 +++ b/test-data/features_test7.tabular Fri Mar 22 08:16:20 2019 -0400 |
| b |
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