diff msi_qualitycontrol.xml @ 15:2d69460669ae draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 620a469e20836b921b6c0147421c8a4268b66ebd

--- 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)