Mercurial > repos > proteore > proteore_pathview_mapping

comparison PathView.R @ 10:e8d6e50f5d38 draft

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planemo upload commit 0be58bb700f64de6792a7234a11675bae2755e8f-dirty
author proteore
date Thu, 13 Sep 2018 03:25:04 -0400
parents 560541195c3f
children
comparison
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9:560541195c3f 10:e8d6e50f5d38
202 low_color = "green" 202 low_color = "green"
203 mid_color = "#F3F781" #yellow 203 mid_color = "#F3F781" #yellow
204 high_color = "red" 204 high_color = "red"
205 if (is.null(tab$e1)) { 205 if (is.null(tab$e1)) {
206 plot.col.key= FALSE #if there's no exrepession data, we don't show the color key 206 plot.col.key= FALSE #if there's no exrepession data, we don't show the color key
207 high_color = "#81F7F3" #blue 207 high_color = "#81BEF7" #blue
208 } 208 }
209 209
210 for (id in ids) { 210 for (id in ids) {
211 pathview(gene.data = mat, 211 pathview(gene.data = mat,
212 pathway.id = id, 212 pathway.id = id,
215 gene.idtype = "entrez", 215 gene.idtype = "entrez",
216 kegg.native = native_kegg, 216 kegg.native = native_kegg,
217 low = list(gene = low_color, cpd = "blue"), 217 low = list(gene = low_color, cpd = "blue"),
218 mid = list(gene = mid_color, cpd = "transparent"), 218 mid = list(gene = mid_color, cpd = "transparent"),
219 high = list(gene = high_color, cpd = "yellow"), 219 high = list(gene = high_color, cpd = "yellow"),
220 na.col="#A4A4A4", #gray 220 na.col="#D8D8D8", #gray
221 cpd.data=NULL, 221 cpd.data=NULL,
222 plot.col.key = plot.col.key, 222 plot.col.key = plot.col.key,
223 pdf.size=c(9,9)) 223 pdf.size=c(9,9))
224 } 224 }
225 225