changeset 5:f0d1f3e97303 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e938d5bf0087479d893ac3889db4ea5ef87a471c"

--- a/quality_report.xml	Fri Mar 22 08:11:43 2019 -0400
+++ b/quality_report.xml	Fri Sep 06 03:40:23 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="cardinal_quality_report" name="MSI Qualitycontrol" version="@VERSION@.3">
+<tool id="cardinal_quality_report" name="MSI Qualitycontrol" version="@VERSION@.4">
     <description>
         mass spectrometry imaging QC
     </description>
@@ -383,7 +383,7 @@
 
     print(ggplot(TICcoordarray, aes(x=x, y=y, fill=TICs))+
      geom_tile() + coord_fixed() +
-     ggtitle("Total Ion Chromatogram")+
+     ggtitle("Total Ion Current")+
      theme_bw() +
      theme(plot.title = element_text(hjust = 0.5))+
      theme(text=element_text(family="ArialMT", face="bold", size=12))+
@@ -534,7 +534,7 @@
     }
 
     title(xlab="Spectra index", line=3)
-    title(ylab = "Total ion chromatogram intensity", line=4)
+    title(ylab = "Total ion current intensity", line=4)
     if (!is.null(levels(msidata\$annotation))){
         abline(v=abline_vector, lty = 3)}
 
@@ -773,7 +773,7 @@
             abline(v=c(mzvalue), col="green2", lty=4)
             ## average plot including points per data point
             plot(msidata_no_NA[minmasspixel1:maxmasspixel1,], pixel = 1:length(pixelnumber), main="Average spectrum with data points")
-            points(mz(msidata_no_NA[minmasspixel1:maxmasspixel1,]), rowMeans(spectra(msidata_no_NA)[minmasspixel1:maxmasspixel1,]), col="blue", pch=20)
+            points(mz(msidata_no_NA[minmasspixel1:maxmasspixel1,]), rowMeans(spectra(msidata_no_NA)[minmasspixel1:maxmasspixel1,,drop=FALSE]), col="blue", pch=20)
             ## plot of third average plot
             plot(msidata_no_NA[minmasspixel2:maxmasspixel2,], pixel = 1:length(pixelnumber), main= "Average spectrum")
             abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))
@@ -1062,7 +1062,7 @@
 - (FC): this plots will only be drawn if the optional fold change image is selected
 - 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.
 
-- 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). 
+- 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). 
 
 **x-y images (pixel/spectra information)**
 
@@ -1073,7 +1073,7 @@
 - (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. 
 - (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). 
 - Number of peaks per spectrum: For each spectrum the number of m/z values with intensity > 0 is calculated and plotted as heatmap.
-- Total ion chromatogram: For each spectrum all intensities are summed up to obtain the TIC which is plotted as heatmap. 
+- Total ion current: For each spectrum all intensities are summed up to obtain the TIC which is plotted as heatmap. 
 - Median intensity: For each spectrum the median intensity is plotted as heatmap. 
 - Maximum intensity: For each spectrum the maximum intensity is plotted as heatmap. 
 - Most abundant m/z in each spectrum: For each spectrum the m/z value with the highest intensity is plotted.