| Previous changeset 10:f365bad862c9 (2020-09-24) Next changeset 12:ecaebe7c7b54 (2020-10-06) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a" |
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modified:
macros.xml quality_report.xml 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/imzml_filtered3.pdf test-data/imzml_filtered4.pdf test-data/imzml_filtered5.pdf test-data/imzml_filtered8.pdf 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/out8.ibd test-data/out8.imzml test-data/out8.imzml.txt test-data/rdata_notfiltered.pdf |
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| diff -r f365bad862c9 -r f396c176f366 macros.xml --- a/macros.xml Thu Sep 24 11:44:48 2020 +0000 +++ b/macros.xml Sun Sep 27 11:11:53 2020 +0000 |
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| @@ -117,6 +117,13 @@ <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[ ########################### QC numbers ######################## ## including intensity calculations which need data in RAM + + int_matrix = as.matrix(spectra(msidata)) ## only load once into RAM, then re-use + ## Number of NA in spectra matrix + NAcount = sum(is.na(int_matrix)) + ## replace NA with zero to calculate data properties based on intensity matrix, no change in msidata + int_matrix[is.na(int_matrix)] <- 0 + ## Number of features (mz) maxfeatures = length(features(msidata)) ## Range mz @@ -131,14 +138,12 @@ minimumy = min(coord(msidata)[,2]) maximumy = max(coord(msidata)[,2]) ## Range of intensities - minint = round(min(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2) - maxint = round(max(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2) + minint = round(min(int_matrix), digits=2) + maxint = round(max(int_matrix), digits=2) ## Number of intensities > 0, for if conditions - npeaks= sum(as.matrix(spectra(msidata))>0, na.rm=TRUE) + npeaks= sum(int_matrix>0) ## Number of NA in spectra matrix - NAcount = sum(is.na(spectra(msidata))) - ## Number of NA in spectra matrix - infcount = sum(is.infinite(as.matrix(spectra(msidata)))) + infcount = sum(is.infinite(int_matrix)) ## Number of duplicated coordinates dupl_coord = sum(duplicated(coord(msidata))) properties = c("Number of m/z features", |
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| diff -r f365bad862c9 -r f396c176f366 quality_report.xml --- a/quality_report.xml Thu Sep 24 11:44:48 2020 +0000 +++ b/quality_report.xml Sun Sep 27 11:11:53 2020 +0000 |
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| b'@@ -60,21 +60,22 @@\n merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)\n merged_annotation[is.na(merged_annotation)] = "NA"\n merged_annotation = merged_annotation[order(merged_annotation\\$pixel_index),]\n- msidata\\$annotation = as.factor(merged_annotation[,4])\n+ msidata\\$annotation = as.character(merged_annotation[,4])\n \n #end if\n \n ###################### calculation of data properties ################################\n @DATA_PROPERTIES_INRAM@\n \n+\n ## Median intensities\n-medint = round(median(spectra(msidata), na.rm=TRUE), digits=2)\n+medint = round(median(int_matrix), digits=2)\n ## Spectra multiplied with m/z (potential number of peaks)\n-numpeaks = ncol(msidata)*nrow(msidata)\n+numpeaks = as.numeric(ncol(msidata)*nrow(msidata))\n ## Percentage of intensities > 0\n percpeaks = round(npeaks/numpeaks*100, digits=2)\n ## Number of empty TICs\n-TICs = pixelApply(msidata, sum)\n+TICs = pixelApply(msidata, sum, na.rm=TRUE)\n NumemptyTIC = sum(TICs == 0)\n ## Median und sd TIC\n medTIC = round(median(TICs), digits=1)\n@@ -183,12 +184,13 @@\n \n ### only for previously combined data, same plot as in combine QC pdf\n \n- if (!is.null(levels(msidata\\$annotation))){\n+ if (!is.null(unique(msidata\\$annotation))){\n \n- number_combined = length(levels(msidata\\$annotation))\n+ number_combined = length(unique(msidata\\$annotation))\n \n position_df = data.frame(coord(msidata)\\$x, coord(msidata)\\$y, msidata\\$annotation)\n colnames(position_df) = c("x", "y","annotation")\n+ print(position_df)\n \n combine_plot = ggplot(position_df, aes(x=x, y=y, fill=annotation))+\n geom_tile() +\n@@ -414,7 +416,7 @@\n \n ############################### 6b) median int image ###############################\n \n- median_int = pixelApply(msidata, median)\n+ median_int = pixelApply(msidata, median, na.rm=TRUE)\n \n median_coordarray=data.frame(coord(msidata)\\$x, coord(msidata)\\$y, median_int)\n colnames(median_coordarray) = c("x", "y", "median_int")\n@@ -433,7 +435,7 @@\n \n ############################### 6c) max int image ###############################\n \n- max_int = pixelApply(msidata, max)\n+ max_int = pixelApply(msidata, max, na.rm=TRUE)\n \n max_coordarray=data.frame(coord(msidata)\\$x, coord(msidata)\\$y, max_int)\n colnames(max_coordarray) = c("x", "y", "max_int")\n@@ -495,7 +497,7 @@\n par(oma=c(0,0,0,1))## margin for image legend\n print(image(pca, column = "PC1" , strip=FALSE, superpose = FALSE, main="PC1", col.regions = risk.colors(100), layout=c(2,1), ylim= c(maximumy+0.2*maximumy,minimumy-1)))\n print(image(pca, column = "PC2" , strip=FALSE, superpose = FALSE, main="PC2", col.regions = risk.colors(100), layout=FALSE, ylim= c(maximumy+0.2*maximumy,minimumy-1)))\n- ## remove pca to clean up RAM space\n+ \t## remove pca to clean up space\n rm(pca)\n gc()\n \n@@ -513,7 +515,7 @@\n title(xlab="Spectra index", line=3)\n title(ylab="Number of peaks", line=4)\n \n- if (!is.null(levels(msidata\\$annotation))){\n+ if (!is.null(unique(msidata\\$annotation))){\n abline(v=abline_vector, lty = 3)}\n \n ## 9b) histogram\n@@ -525,11 +527,11 @@\n \n ## 9c) additional histogram to show contribution of annotation groups\n \n- if (!is.null(levels(msidata\\$annotation))){\n+ if (!is.null(unique(msidata\\$annotation))){\n \n df_9 = data.frame(peaksperpixel, msidata\\$annotation)\n colnames(df_9) = c("Npeaks", "annotation")\n-\n+ \n hist_9 = ggplot(df_9, aes(x=Npeaks, fill=annotation)) +\n geom_histogram()+ theme_bw()+\n theme(text=element_text(family="ArialMT", face="bold", size=12))+\n@@ -555,17 +557,17 @@\n \n title(xlab="Spectra index", line=3)\n title(ylab = "Total ion current intensity", line=4)\n- if (!is.null(levels(msidata\\$annotation))){\n+ if (!is.null(unique(msidata\\$annotation))){\n abline(v=abline_vector, lty = 3)}\n \n ## 10b) histo'..b'erpose=TRUE, main="Average mass spectra for annotation groups"))\n+ print(plot(msidata, run="infile", pixel.groups=msidata\\$annotation, key=key_legend, col=hue_pal()(length(unique(msidata\\$annotation))),superpose=TRUE, main="Average mass spectra for annotation groups"))\n }\n \n ## plot 4 random mass spectra\n@@ -742,7 +744,7 @@\n pixel_vector = sample(which(TICs != 0),4)\n \n par(mfrow = c(2, 2), cex.axis=1, cex.lab=1, mar=c(5.1,4.1,4.1,2.1))\n- print(plot(msidata_no_NA, pixel = pixel_vector))\n+ print(plot(msidata_no_NA, pixel = pixel_vector, col="black"))\n \n \n ################### 16) Zoomed in mass spectra for calibrants ##############\n@@ -790,20 +792,20 @@\n par(oma=c(0,0,2,0))\n ## average plot\n \n- print(plot(msidata_no_NA[minmasspixel1:maxmasspixel1,], run="infile", layout=c(2,2), strip=FALSE, main= "Average spectrum"))\n+ print(plot(msidata_no_NA[minmasspixel1:maxmasspixel1,], run="infile", layout=c(2,2), strip=FALSE, main= "Average spectrum", col="black"))\n abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))\n abline(v=c(maxvalue), col="red", lty=2)\n abline(v=c(mzvalue), col="green2", lty=4)\n ## average plot including points per data point\n- print(plot(msidata_no_NA[minmasspixel1:maxmasspixel1,], run="infile", layout=FALSE, strip=FALSE, main="Average spectrum with data points"))\n+ print(plot(msidata_no_NA[minmasspixel1:maxmasspixel1,], run="infile", layout=FALSE, strip=FALSE, main="Average spectrum with data points", col="black"))\n points(mz(msidata_no_NA[minmasspixel1:maxmasspixel1,]), rowMeans(spectra(msidata_no_NA)[minmasspixel1:maxmasspixel1,,drop=FALSE]), col="blue", pch=20)\n ## plot of third average plot\n- print(plot(msidata_no_NA[minmasspixel2:maxmasspixel2,], run="infile", layout=FALSE, strip=FALSE, main= "Average spectrum"))\n+ print(plot(msidata_no_NA[minmasspixel2:maxmasspixel2,], run="infile", layout=FALSE, strip=FALSE, main= "Average spectrum", col="black"))\n abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))\n abline(v=c(maxvalue), col="red", lty=2)\n abline(v=c(mzvalue), col="green2", lty=4)\n ## plot of fourth average plot\n- print(plot(msidata_no_NA[minmasspixel3:maxmasspixel3,], run="infile", layout=FALSE, strip=FALSE, main= "Average spectrum"))\n+ print(plot(msidata_no_NA[minmasspixel3:maxmasspixel3,], run="infile", layout=FALSE, strip=FALSE, main= "Average spectrum", col="black"))\n abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))\n abline(v=c(maxvalue), col="red", lty=2)\n abline(v=c(mzvalue), col="green2", lty=4)\n@@ -813,7 +815,7 @@\n \n ### 16b) one large extra plot with different colours for different pixel annotation groups\n \n- if (!is.null(levels(msidata\\$annotation))){\n+ if (!is.null(unique(msidata\\$annotation))){\n if (number_combined < 10){\n key_zoomed = TRUE\n }else{key_zoomed = FALSE}\n@@ -910,7 +912,7 @@\n for (each_cal in 1:ncol(ppm_df)){\n lines(ppm_df[,each_cal], col=mycolours[each_cal], type="p")}\n legend("topright", inset=c(-0.2,0), xpd = TRUE, bty="n", cex=0.8,legend=inputcalibrantmasses, col=mycolours[1:ncol(ppm_df)],lty=1)\n- if (!is.null(levels(msidata\\$annotation))){\n+ if (!is.null(unique(msidata\\$annotation))){\n abline(v=abline_vector, lty = 3)}}\n \n ### make x-y-images for mz accuracy\n' |
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| @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="c6cc990a-d910-4c17-aedd-ceb204b4d105" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="ef8c4f864d0386736c986ebb4d4eb29a726e42d4" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="97f42eea-750c-49e4-b46d-08c548dc3b9d" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="4e046226f81e9c78255df625ca3546ef26dd0693" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r f365bad862c9 -r f396c176f366 test-data/out3.imzml.txt --- a/test-data/out3.imzml.txt Thu Sep 24 11:44:48 2020 +0000 +++ b/test-data/out3.imzml.txt Sun Sep 27 11:11:53 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 24 --rw-rw-r-- 1 meli meli 9616 Aug 23 17:39 ibd --rw-rw-r-- 1 meli meli 8958 Aug 23 17:39 imzml +-rw-rw-r-- 1 meli meli 9616 Sep 27 10:51 ibd +-rw-rw-r-- 1 meli meli 8958 Sep 27 10:51 imzml |
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| @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="78fa5a7c-8dc8-4ff1-ad77-b19714f285cb" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="64d40f8c65af1399e24d94569f4dd3fdbf43a901" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="37f3f75a-82c4-47c5-b78e-28fb8697e59b" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="1746fd2ec8a12707330a78ff5a0ff98cb53dca42" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| @@ -1,4 +1,4 @@ imzML file: total 44 --rw-rw-r-- 1 meli meli 28792 Aug 23 17:39 ibd --rw-rw-r-- 1 meli meli 12046 Aug 23 17:39 imzml +-rw-rw-r-- 1 meli meli 28792 Sep 27 10:52 ibd +-rw-rw-r-- 1 meli meli 12046 Sep 27 10:52 imzml |
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| @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="30751422-deca-429e-9f8e-24639c108d6d" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="2c7f19c6447844039a112152c19f7cfd50dbf12e" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="37236c7e-6e93-4ccc-9111-1b1153aac713" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="ccb886aaf3cb7564f518884413ea988c59a1de57" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r f365bad862c9 -r f396c176f366 test-data/out5.imzml.txt --- a/test-data/out5.imzml.txt Thu Sep 24 11:44:48 2020 +0000 +++ b/test-data/out5.imzml.txt Sun Sep 27 11:11:53 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 20 --rw-rw-r-- 1 meli meli 380 Aug 23 17:40 ibd --rw-rw-r-- 1 meli meli 13525 Aug 23 17:40 imzml +-rw-rw-r-- 1 meli meli 380 Sep 27 10:53 ibd +-rw-rw-r-- 1 meli meli 13525 Sep 27 10:53 imzml |
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| @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="254b991f-92f5-46d5-8069-6f9ecd53b05a" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0aaa784dc2a335da176a4bc2d12a43f2d18bdbf1" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="734d4b50-4440-4747-a0e9-de78974d1487" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="b1636b28fd4e0ab9caf5aaa4c1a40760030a4e73" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| @@ -1,4 +1,4 @@ imzML file: total 164 --rw-rw-r-- 1 meli meli 146896 Aug 23 17:41 ibd --rw-rw-r-- 1 meli meli 18221 Aug 23 17:41 imzml +-rw-rw-r-- 1 meli meli 146896 Sep 27 10:53 ibd +-rw-rw-r-- 1 meli meli 18221 Sep 27 10:53 imzml |
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| @@ -1,4 +1,4 @@ imzML file: total 116 --rw-rw-r-- 1 meli meli 95976 Aug 23 17:41 ibd --rw-rw-r-- 1 meli meli 18199 Aug 23 17:41 imzml +-rw-rw-r-- 1 meli meli 95976 Sep 27 10:54 ibd +-rw-rw-r-- 1 meli meli 18199 Sep 27 10:54 imzml |
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| diff -r f365bad862c9 -r f396c176f366 test-data/out8.imzml --- a/test-data/out8.imzml Thu Sep 24 11:44:48 2020 +0000 +++ b/test-data/out8.imzml Sun Sep 27 11:11:53 2020 +0000 |
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| diff -r f365bad862c9 -r f396c176f366 test-data/out8.imzml.txt --- a/test-data/out8.imzml.txt Thu Sep 24 11:44:48 2020 +0000 +++ b/test-data/out8.imzml.txt Sun Sep 27 11:11:53 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: -total 348 --rw-rw-r-- 1 meli meli 335976 Aug 23 17:42 ibd --rw-rw-r-- 1 meli meli 12402 Aug 23 17:42 imzml +total 260 +-rw-rw-r-- 1 meli meli 248824 Sep 27 11:44 ibd +-rw-rw-r-- 1 meli meli 12397 Sep 27 11:44 imzml |
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| diff -r f365bad862c9 -r f396c176f366 test-data/rdata_notfiltered.pdf |
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| Binary file test-data/rdata_notfiltered.pdf has changed |