diff quality_report.xml @ 3:16556ca0196b draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2

--- a/quality_report.xml	Fri Feb 15 10:21:09 2019 -0500
+++ b/quality_report.xml	Thu Feb 28 09:26:25 2019 -0500
@@ -898,7 +898,7 @@
                  theme_bw() +
                  theme(plot.title = element_text(hjust = 0.5))+
                  theme(text=element_text(family="ArialMT", face="bold", size=12))+
-                 scale_fill_gradient2(low = "navy", mid = "white", high = "red", midpoint = 0 ,space = "Lab", na.value = "black", name = "ppm\nerror"))}
+                 scale_fill_gradient2(low = "navy", mid = "grey", high = "red", midpoint = 0 ,space = "Lab", na.value = "black", name = "ppm\nerror"))}
 
 
     }else{print("plot 16+17+18+19) The inputcalibrant m/z were not provided or outside the m/z range")}
@@ -1064,7 +1064,7 @@
 - (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. 
 - (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. 
 - (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. The intensities are averaged within the calibrant m/z window (ppm range). 
+- (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. 
 - Median intensity: For each spectrum the median intensity is plotted as heatmap.