# HG changeset patch
# User galaxyp
# Date 1536082924 14400
# Node ID ebca696cb0240086c27af629855fb202ff84176f
# Parent  d0e13a160a6c187b640f754e28d30abda9f40c73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit e87eea03505ab1ba067e192bbbcdc6197dc4b42e

diff -r d0e13a160a6c -r ebca696cb024 msi_spectra_plots.xml
--- a/msi_spectra_plots.xml	Wed Aug 22 13:44:57 2018 -0400
+++ b/msi_spectra_plots.xml	Tue Sep 04 13:42:04 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.6">
+<tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.7">
     <description>
         mass spectrometry imaging mass spectra plots
     </description>
@@ -120,7 +120,7 @@
                "Range of intensities", 
                "Median of intensities",
                "Intensities > 0",
-               "Number of zero TICs",
+               "Number of empty spectra",
                "Preprocessing", 
                "Normalization", 
                "Smoothing",
@@ -265,19 +265,26 @@
                         legend_size = 6
                     }
 
-                    position_df = cbind(coord(msidata)[,1:2], msidata\$annotation)
+                    position_df = cbind(coord(msidata)[,1:2], as.factor(msidata\$annotation))
                     colnames(position_df)[3] = "sample_name"
 
                     combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
-                           geom_tile() +
+                           geom_tile(height = 1, width=1)+
                            coord_fixed()+
                            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))+
                            theme(legend.position="bottom",legend.direction="vertical")+
-                           theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
-                           guides(fill=guide_legend(ncol=5,byrow=TRUE))
+                           theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 6))+
+                           guides(fill=guide_legend(ncol=4,byrow=TRUE))
+
+                   coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
+                   coord_labels\$file_number = 1:length(levels(position_df\$sample_name))
+
+                    for(file_count in 1:nrow(coord_labels))
+                    {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
+                    y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
 
                     print(combine_plot)
 
diff -r d0e13a160a6c -r ebca696cb024 test-data/Plot_analyze75.pdf
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diff -r d0e13a160a6c -r ebca696cb024 test-data/Plot_analyze75_allpixels.pdf
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diff -r d0e13a160a6c -r ebca696cb024 test-data/Plot_empty_spectra.pdf
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diff -r d0e13a160a6c -r ebca696cb024 test-data/Plot_imzml.pdf
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diff -r d0e13a160a6c -r ebca696cb024 test-data/Plot_rdata.pdf
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