comparison quality_report.xml @ 3:16556ca0196b draft

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

2:d4803c1e5e19

                 geom_tile() + coord_fixed() +
                 ggtitle(paste0("m/z accuracy for ",inputcalibrants[,2][each_cal]))+
                 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"))}


    }else{print("plot 16+17+18+19) The inputcalibrant m/z were not provided or outside the m/z range")}
}else{
    print("inputfile has no intensities > 0")

- (annot) Spatial orientation of annotated pixel: All pixels of one annotation group have the same colour. 
- 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. 
- (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). 
- 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. 
- 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. 

3:16556ca0196b

                 geom_tile() + coord_fixed() +
                 ggtitle(paste0("m/z accuracy for ",inputcalibrants[,2][each_cal]))+
                 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 = "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")}
}else{
    print("inputfile has no intensities > 0")

- (annot) Spatial orientation of annotated pixel: All pixels of one annotation group have the same colour. 
- 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. 
- (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 (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. 
- 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.