Mercurial > repos > galaxyp > cardinal_quality_report

comparison quality_report.xml @ 5:f0d1f3e97303 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e938d5bf0087479d893ac3889db4ea5ef87a471c"
author galaxyp
date Fri, 06 Sep 2019 03:40:23 -0400
parents 3b7a35d50ebf
children bb9500286fe4
comparison
equal deleted inserted replaced
4:3b7a35d50ebf 5:f0d1f3e97303
1 <tool id="cardinal_quality_report" name="MSI Qualitycontrol" version="@VERSION@.3"> 1 <tool id="cardinal_quality_report" name="MSI Qualitycontrol" version="@VERSION@.4">
2 <description> 2 <description>
3 mass spectrometry imaging QC 3 mass spectrometry imaging QC
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
381 381
382 TICcoordarray=cbind(coord(msidata)[,1:2], TICs) 382 TICcoordarray=cbind(coord(msidata)[,1:2], TICs)
383 383
384 print(ggplot(TICcoordarray, aes(x=x, y=y, fill=TICs))+ 384 print(ggplot(TICcoordarray, aes(x=x, y=y, fill=TICs))+
385 geom_tile() + coord_fixed() + 385 geom_tile() + coord_fixed() +
386 ggtitle("Total Ion Chromatogram")+ 386 ggtitle("Total Ion Current")+
387 theme_bw() + 387 theme_bw() +
388 theme(plot.title = element_text(hjust = 0.5))+ 388 theme(plot.title = element_text(hjust = 0.5))+
389 theme(text=element_text(family="ArialMT", face="bold", size=12))+ 389 theme(text=element_text(family="ArialMT", face="bold", size=12))+
390 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange") 390 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
391 ,space = "Lab", na.value = "black", name = "TIC")) 391 ,space = "Lab", na.value = "black", name = "TIC"))
532 }else{ 532 }else{
533 plot_colorByDensity(pixels(msidata), TICs, ylab = "", xlab = "", main="TIC per spectrum") 533 plot_colorByDensity(pixels(msidata), TICs, ylab = "", xlab = "", main="TIC per spectrum")
534 } 534 }
535 535
536 title(xlab="Spectra index", line=3) 536 title(xlab="Spectra index", line=3)
537 title(ylab = "Total ion chromatogram intensity", line=4) 537 title(ylab = "Total ion current intensity", line=4)
538 if (!is.null(levels(msidata\$annotation))){ 538 if (!is.null(levels(msidata\$annotation))){
539 abline(v=abline_vector, lty = 3)} 539 abline(v=abline_vector, lty = 3)}
540 540
541 ## 10b) histogram 541 ## 10b) histogram
542 hist((TICs), main="", las=1, xlab = "TIC per spectrum", ylab="") 542 hist((TICs), main="", las=1, xlab = "TIC per spectrum", ylab="")
771 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3)) 771 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))
772 abline(v=c(maxvalue), col="red", lty=2) 772 abline(v=c(maxvalue), col="red", lty=2)
773 abline(v=c(mzvalue), col="green2", lty=4) 773 abline(v=c(mzvalue), col="green2", lty=4)
774 ## average plot including points per data point 774 ## average plot including points per data point
775 plot(msidata_no_NA[minmasspixel1:maxmasspixel1,], pixel = 1:length(pixelnumber), main="Average spectrum with data points") 775 plot(msidata_no_NA[minmasspixel1:maxmasspixel1,], pixel = 1:length(pixelnumber), main="Average spectrum with data points")
776 points(mz(msidata_no_NA[minmasspixel1:maxmasspixel1,]), rowMeans(spectra(msidata_no_NA)[minmasspixel1:maxmasspixel1,]), col="blue", pch=20) 776 points(mz(msidata_no_NA[minmasspixel1:maxmasspixel1,]), rowMeans(spectra(msidata_no_NA)[minmasspixel1:maxmasspixel1,,drop=FALSE]), col="blue", pch=20)
777 ## plot of third average plot 777 ## plot of third average plot
778 plot(msidata_no_NA[minmasspixel2:maxmasspixel2,], pixel = 1:length(pixelnumber), main= "Average spectrum") 778 plot(msidata_no_NA[minmasspixel2:maxmasspixel2,], pixel = 1:length(pixelnumber), main= "Average spectrum")
779 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3)) 779 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))
780 abline(v=c(maxvalue), col="red", lty=2) 780 abline(v=c(maxvalue), col="red", lty=2)
781 abline(v=c(mzvalue), col="green2", lty=4) 781 abline(v=c(mzvalue), col="green2", lty=4)
1060 - (annot): this plots will only be drawn if pixel annotations are loaded via a tabular file 1060 - (annot): this plots will only be drawn if pixel annotations are loaded via a tabular file
1061 - (cal): this plots will only be drawn if a tabular file with at least one valid calibrant m/z is provided 1061 - (cal): this plots will only be drawn if a tabular file with at least one valid calibrant m/z is provided
1062 - (FC): this plots will only be drawn if the optional fold change image is selected 1062 - (FC): this plots will only be drawn if the optional fold change image is selected
1063 - Vertical lines in histograms represent median values. In density scatter plots the colour changes from blue to green, yellow and red the more points are overlayed. 1063 - Vertical lines in histograms represent median values. In density scatter plots the colour changes from blue to green, yellow and red the more points are overlayed.
1064 1064
1065 - Overview of file properties: Numbers and ranges for m/z features and pixels are given. Median and range across all intensity values are provided. Intensities > 0 gives the percentage of m/z-pixel pairs with an intensity above zero. The number of empty spectra (TIC = 0), the median number of peaks (intensities > 0) per spectra as well as the median TIC (total ion chromatogram) are given. The processing status of the file is provided as well as the number of valid calibrants from the provided tabular file.> 0 (Intensities > 0). 1065 - Overview of file properties: Numbers and ranges for m/z features and pixels are given. Median and range across all intensity values are provided. Intensities > 0 gives the percentage of m/z-pixel pairs with an intensity above zero. The number of empty spectra (TIC = 0), the median number of peaks (intensities > 0) per spectra as well as the median TIC (total ion current) are given. The processing status of the file is provided as well as the number of valid calibrants from the provided tabular file.> 0 (Intensities > 0).
1066 1066
1067 **x-y images (pixel/spectra information)** 1067 **x-y images (pixel/spectra information)**
1068 1068
1069 - (annot) Spatial orientation of annotated pixel: All pixels of one annotation group have the same colour. 1069 - (annot) Spatial orientation of annotated pixel: All pixels of one annotation group have the same colour.
1070 - Pixel order: Shows the order of the pixels in the provided file. Depending on the instrument this can represent the acquisition order. If annotation file is provided pixels are ordered according to annotation groups. 1070 - Pixel order: Shows the order of the pixels in the provided file. Depending on the instrument this can represent the acquisition order. If annotation file is provided pixels are ordered according to annotation groups.
1071 - (cal) Number of calibrants per pixel: In every spectrum the calibrant m/z window (calibrant m/z plusminus 'ppm range') is searched for peaks (intensity > 0). Calibrants are considered present in a spectrum when they have at least one peak in their m/z window. 1071 - (cal) Number of calibrants per pixel: In every spectrum the calibrant m/z window (calibrant m/z plusminus 'ppm range') is searched for peaks (intensity > 0). Calibrants are considered present in a spectrum when they have at least one peak in their m/z window.
1072 - (FC) Control of fold change plot: For both input m/z a zoomed in average spectrum is drawn with the input m/z as blue dashed line, the m/z range as blue dotted lines and the maximum intensity in the m/z window with a red line. 1072 - (FC) Control of fold change plot: For both input m/z a zoomed in average spectrum is drawn with the input m/z as blue dashed line, the m/z range as blue dotted lines and the maximum intensity in the m/z window with a red line.
1073 - (FC) Fold change image: For each input m/z the average intensity within the given ppm range is calculated, then the log2 fold change of both average intensities is taken and plotted as heatmap. 1073 - (FC) Fold change image: For each input m/z the average intensity within the given ppm range is calculated, then the log2 fold change of both average intensities is taken and plotted as heatmap.
1074 - (cal) Intensity heatmaps for the m/z value that is closest to the calibrant m/z (can be outside the ppm range). The intensities are averaged within the calibrant m/z window (ppm range). 1074 - (cal) Intensity heatmaps for the m/z value that is closest to the calibrant m/z (can be outside the ppm range). The intensities are averaged within the calibrant m/z window (ppm range).
1075 - Number of peaks per spectrum: For each spectrum the number of m/z values with intensity > 0 is calculated and plotted as heatmap. 1075 - Number of peaks per spectrum: For each spectrum the number of m/z values with intensity > 0 is calculated and plotted as heatmap.
1076 - Total ion chromatogram: For each spectrum all intensities are summed up to obtain the TIC which is plotted as heatmap. 1076 - Total ion current: For each spectrum all intensities are summed up to obtain the TIC which is plotted as heatmap.
1077 - Median intensity: For each spectrum the median intensity is plotted as heatmap. 1077 - Median intensity: For each spectrum the median intensity is plotted as heatmap.
1078 - Maximum intensity: For each spectrum the maximum intensity is plotted as heatmap. 1078 - Maximum intensity: For each spectrum the maximum intensity is plotted as heatmap.
1079 - Most abundant m/z in each spectrum: For each spectrum the m/z value with the highest intensity is plotted. 1079 - Most abundant m/z in each spectrum: For each spectrum the m/z value with the highest intensity is plotted.
1080 - PCA for two components: Result of a principal component analysis (PCA) for two components is given. The loading plot depicts the contribution of each m/z value and the x-y image represents the differences between the pixels, principal components 1 and 2 are also plotted as x-y image. 1080 - PCA for two components: Result of a principal component analysis (PCA) for two components is given. The loading plot depicts the contribution of each m/z value and the x-y image represents the differences between the pixels, principal components 1 and 2 are also plotted as x-y image.
1081 1081