Mercurial > repos > galaxyp > msi_spectra_plot

comparison msi_spectra_plots.xml @ 9:ebca696cb024 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit e87eea03505ab1ba067e192bbbcdc6197dc4b42e
author galaxyp
date Tue, 04 Sep 2018 13:42:04 -0400
parents d0e13a160a6c
children
comparison
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8:d0e13a160a6c 9:ebca696cb024
1 <tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.6"> 1 <tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.7">
2 <description> 2 <description>
3 mass spectrometry imaging mass spectra plots 3 mass spectrometry imaging mass spectra plots
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> 6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
118 "Range of x coordinates", 118 "Range of x coordinates",
119 "Range of y coordinates", 119 "Range of y coordinates",
120 "Range of intensities", 120 "Range of intensities",
121 "Median of intensities", 121 "Median of intensities",
122 "Intensities > 0", 122 "Intensities > 0",
123 "Number of zero TICs", 123 "Number of empty spectra",
124 "Preprocessing", 124 "Preprocessing",
125 "Normalization", 125 "Normalization",
126 "Smoothing", 126 "Smoothing",
127 "Baseline reduction", 127 "Baseline reduction",
128 "Peak picking", 128 "Peak picking",
263 legend_size = 7 263 legend_size = 7
264 }else{ 264 }else{
265 legend_size = 6 265 legend_size = 6
266 } 266 }
267 267
268 position_df = cbind(coord(msidata)[,1:2], msidata\$annotation) 268 position_df = cbind(coord(msidata)[,1:2], as.factor(msidata\$annotation))
269 colnames(position_df)[3] = "sample_name" 269 colnames(position_df)[3] = "sample_name"
270 270
271 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+ 271 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
272 geom_tile() + 272 geom_tile(height = 1, width=1)+
273 coord_fixed()+ 273 coord_fixed()+
274 ggtitle("Spatial orientation of pixel annotations")+ 274 ggtitle("Spatial orientation of pixel annotations")+
275 theme_bw()+ 275 theme_bw()+
276 theme(plot.title = element_text(hjust = 0.5))+ 276 theme(plot.title = element_text(hjust = 0.5))+
277 theme(text=element_text(family="ArialMT", face="bold", size=12))+ 277 theme(text=element_text(family="ArialMT", face="bold", size=12))+
278 theme(legend.position="bottom",legend.direction="vertical")+ 278 theme(legend.position="bottom",legend.direction="vertical")+
279 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+ 279 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 6))+
280 guides(fill=guide_legend(ncol=5,byrow=TRUE)) 280 guides(fill=guide_legend(ncol=4,byrow=TRUE))
281
282 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
283 coord_labels\$file_number = 1:length(levels(position_df\$sample_name))
284
285 for(file_count in 1:nrow(coord_labels))
286 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
287 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
281 288
282 print(combine_plot) 289 print(combine_plot)
283 290
284 ## print legend only for less than 10 samples 291 ## print legend only for less than 10 samples
285 if (length(levels(msidata\$annotation)) < 10){ 292 if (length(levels(msidata\$annotation)) < 10){