Mercurial > repos > galaxyp > msi_qualitycontrol
changeset 15:2d69460669ae draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 620a469e20836b921b6c0147421c8a4268b66ebd
| author | galaxyp |
|---|---|
| date | Wed, 15 Aug 2018 05:40:29 -0400 |
| parents | 7c7c39b9ec4a |
| children | ed23ae226cdc |
| files | msi_qualitycontrol.xml test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf |
| diffstat | 5 files changed, 15 insertions(+), 9 deletions(-) [+] |
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--- a/msi_qualitycontrol.xml Tue Jul 24 04:53:25 2018 -0400 +++ b/msi_qualitycontrol.xml Wed Aug 15 05:40:29 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.10.0.5"> +<tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.10.0.6"> <description> mass spectrometry imaging QC </description> @@ -286,11 +286,16 @@ spectrum_list[[list_count]] = position_df list_count = list_count+1 - colnames(position_df)[3] = "Annotation" - combine_plot = ggplot(position_df, aes(x=x, y=y, fill=Annotation))+ + colnames(position_df)[3] = "annotation" + +print(position_df) +print(class(position_df\$x)) +print(class(position_df\$annotation)) + + combine_plot = ggplot(position_df, aes(x=x, y=y, fill=annotation))+ geom_tile() + coord_fixed()+ - ggtitle("Spatial orientation of combined data")+ + ggtitle("Spatial orientation of pixel annotations")+ theme_bw()+ theme(plot.title = element_text(hjust = 0.5))+ theme(text=element_text(family="ArialMT", face="bold", size=12))+ @@ -844,6 +849,7 @@ ######### 17) ppm difference input calibrant m/z and m/z with max intensity in given m/z range######### + par(mfrow = c(1,1)) ### plot the ppm difference calculated above: theor. m/z value to highest m/z value: calibrant_names = as.character(inputcalibrants[,2]) @@ -851,14 +857,14 @@ if (sum(is.na(diff_df[,1])) == nrow(diff_df)){ plot(0,type='n',axes=FALSE,ann=FALSE) - title(main=paste("plot 17: no peaks in the chosen region, repeat with higher ppm range")) ## here klammer weggenommen... + title(main=paste("plot 17: no peaks in the chosen region, repeat with higher ppm range")) }else{ diff_plot1=ggplot(data=diff_df, aes(x=calibrant_names, y=differencevector)) + geom_bar(stat="identity", fill = "darkgray") + theme_minimal() + labs(title="Average m/z error (max. average intensity vs. theor. calibrant m/z)", x="calibrants", y = "Average m/z error in ppm")+ - theme(plot.title = element_text(hjust = 0.5, size=14))+theme(text=element_text(family="ArialMT", face="bold", size=16))+ + theme(plot.title = element_text(hjust = 0.5, size=14))+theme(text=element_text(family="ArialMT", face="bold", size=14))+ geom_text(aes(label=differencevector), vjust=-0.3, size=5.5, col="blue") + - theme(axis.text.x = element_text(angle = 90, hjust = 1, size=16)) + theme(axis.text.x = element_text(angle = 90, hjust = 1, size=14)) print(diff_plot1) } @@ -873,9 +879,9 @@ diff_plot2=ggplot(data=diff_df, aes(x=calibrant_names, y=differencevector2)) + geom_bar(stat="identity", fill = "darkgray") + theme_minimal() + labs(title="Average m/z error (closest measured m/z vs. theor. calibrant m/z)", x="calibrants", y = "Average m/z error in ppm")+ - theme(plot.title = element_text(hjust = 0.5, size=16))+theme(text=element_text(family="ArialMT", face="bold", size=16))+ + theme(plot.title = element_text(hjust = 0.5, size=14))+theme(text=element_text(family="ArialMT", face="bold", size=14))+ geom_text(aes(label=differencevector2), vjust=-0.3, size=5.5, col="blue")+ - theme(axis.text.x = element_text(angle = 90, hjust = 1, size=16)) + theme(axis.text.x = element_text(angle = 90, hjust = 1, size=14)) print(diff_plot2)