Mercurial > repos > galaxyp > cardinal_spectra_plots
changeset 2:3642ed221eb2 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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--- a/macros.xml Thu Oct 25 07:30:24 2018 -0400 +++ b/macros.xml Fri Feb 15 10:23:28 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>
--- a/spectra_plots.xml Thu Oct 25 07:30:24 2018 -0400 +++ b/spectra_plots.xml Fri Feb 15 10:23:28 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.1"> +<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.2"> <description> mass spectrometry imaging mass spectra plots </description> @@ -27,6 +27,7 @@ library(ggplot2) library(scales) + @READING_MSIDATA@ @DATA_PROPERTIES@ @@ -52,15 +53,17 @@ ## set NA to 0 otherwise plot function will not work - ##spectra(msidata)[is.na(spectra(msidata)[])] = 0 ## in case of NA values they will be set to zero + #if str($processed_cond.processed_file) == "processed": + ##processed file needs to be converted into matrix to be able to replace NAs + iData(msidata) <- iData(msidata)[] + spectra(msidata)[][is.na(spectra(msidata)[])] = 0 + #else + spectra(msidata)[is.na(spectra(msidata))] = 0 + #end if - spectra_df = spectra(msidata)[] - spectra_df[is.na(spectra_df)] = 0 - print(paste0("Number of NA which were converted into 0:",sum(is.na(spectra_df)))) - spectra(msidata) = spectra_df +## run only if mz and pixels are > 0 - -if (npeaks > 0){ +if (ncol(msidata)>0 & nrow(msidata) >0){ pixeldf = data.frame(matrix(ncol = 2, nrow=0)) @@ -73,13 +76,21 @@ #for $chosenpixel in $pixel_conditional.repeatpixel: pixelname = paste0("x = ", $chosenpixel.inputx,", ", "y = ", $chosenpixel.inputy) - pixelisvalid = as.character(pixelname %in% names(pixels(msidata))) + + + + input_pixels = paste($chosenpixel.inputx, $chosenpixel.inputy, sep="_") + dataset_pixels = paste(coord(msidata)\$x, coord(msidata)\$y, sep="_") + + pixelisvalid = as.character(input_pixels %in% dataset_pixels) + + + pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid)) ############################# II) control image #################### if (pixelisvalid == "TRUE"){ - print(pixelisvalid) image(msidata, mz=$chosenpixel.inputmz, ylim = c(maximumy+(0.2*maximumy),minimumy-1), colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton, @@ -188,16 +199,13 @@ key_legend = TRUE }else{key_legend = FALSE} - spectra(msidata)[is.na(spectra(msidata)[])] = 0 ## in case of NA values they will be set to zero plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE) }else{ - spectra(msidata)[is.na(spectra(msidata)[])] = 0 ## in case of NA values they will be set to zero plot(msidata, pixel=1:ncol(msidata), key=TRUE)} ##################### II) Sample: plot zoom-in mass spectrum ########## #if $pixel_conditional.zoomed_sample: - iData(msidata) <- iData(msidata)[] ## getting back data on disk #for $token in $pixel_conditional.zoomed_sample: print("zoomed sample pixels") @@ -317,7 +325,7 @@ </conditional> </inputs> <outputs> - <data format="pdf" name="plots" from_work_dir="mzplots.pdf" label="${tool.name} on ${on_string}"/> + <data format="pdf" name="plots" from_work_dir="mzplots.pdf" label="${tool.name} on ${on_string}:results"/> </outputs> <tests> <test>
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/preprocessing_results1.imzml.txt Fri Feb 15 10:23:28 2019 -0500 @@ -0,0 +1,4 @@ +imzML file: +total 24 +-rw-r--r-- 1 meli meli 96 Feb 12 21:24 ibd +-rw-r--r-- 1 meli meli 16714 Feb 12 21:24 imzml
--- a/test-data/preprocessing_results1.txt Thu Oct 25 07:30:24 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/preprocessing_results4.imzml.txt Fri Feb 15 10:23:28 2019 -0500 @@ -0,0 +1,4 @@ +imzML file: +total 28 +-rw-r--r-- 1 meli meli 6376 Feb 12 21:29 ibd +-rw-r--r-- 1 meli meli 16801 Feb 12 21:29 imzml
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--- a/test-data/scores_pca.tabular Thu Oct 25 07:30:24 2018 -0400 +++ b/test-data/scores_pca.tabular Fri Feb 15 10:23:28 2019 -0500 @@ -1,10 +1,10 @@ pixel names x y PC1 PC2 -xy_1_1 1 1 1.00970093989579 0.757987492163095 -xy_2_1 2 1 0.579669229309751 -0.365615195586663 -xy_3_1 3 1 -1.04790449059337 0.831141108678224 -xy_1_2 1 2 3.5004093695087 0.608578545994517 -xy_2_2 2 2 -0.325050824762022 0.275854508943195 -xy_3_2 3 2 -1.31374997886227 0.0192699346592569 -xy_1_3 1 3 -1.46193831394872 -0.0337353199555284 -xy_2_3 2 3 -1.08833133183905 1.16461090511219 -xy_3_3 3 3 0.147195401291175 -3.25809198000829 +xy_1_1 1 1 1.009701 0.757987 +xy_2_1 2 1 0.579669 -0.365615 +xy_3_1 3 1 -1.047904 0.831141 +xy_1_2 1 2 3.500409 0.608579 +xy_2_2 2 2 -0.325051 0.275855 +xy_3_2 3 2 -1.31375 0.01927 +xy_1_3 1 3 -1.461938 -0.033735 +xy_2_3 2 3 -1.088331 1.164611 +xy_3_3 3 3 0.147195 -3.258092