Hic dev

RLIB/cis_matrix_body_multi.R

@@ -47,7 +47,7 @@ require(plyr, quietly = TRUE)
 require(RColorBrewer, quietly = TRUE)
 require(gridExtra, quietly = TRUE)
 require(grid, quietly = TRUE)
-require(ggplot2 ,quietly = TRUE)
+##require(ggplot2 ,quietly = TRUE)
 require(ggpmisc, quietly = TRUE)
 if ( !(require("ggbio")) ) {
   biocLite("ggbio")
@@ -145,7 +145,7 @@ if(colour_range[2] == 0){
 #}
 
 wh <- GenomicRanges::GRanges(region[["chr"]], IRanges::IRanges(as.integer(region[["start"]]),as.integer(region[["end"]])))
-tset <- ggbio::autoplot(txdb , which = wh, genome.axis = FALSE, names.expr = "tx_name")
+tset <- ggbio::autoplot(txdb , which = wh, genome.axis = FALSE, names.expr = "gene_id")
 p2 <- tset@ggplot
 
 
@@ -154,15 +154,16 @@ palette <- c(
   rgb(0,0,255,maxColorValue=255),
   rgb(152,20,18,maxColorValue=255),
   rgb(240,48,0,maxColorValue=255),
-  rgb(255,188,39,maxColorValue=255))
+  rgb(255,188,39,maxColorValue=255),
+  rgb(124,252,0,maxColorValue=255))
 
 # triangle plot
 message(paste("Constructing plot"))
 p <- ggplot2::ggplot()
 p <- p + geom_polygon(aes(x=x, y=y, group=group), fill="black", data=rotated_bg)
 if(add_borders_to_elements){
   p <- p + geom_polygon(aes(x=x, y=y, group=group, fill=signal, colour=signal), data=rotated_data, size=0.2)
-  p <- p + scale_colour_gradientn(limits=colour_range, colours=palette, na.value = "green")
+  p <- p + scale_colour_gradientn(limits=colour_range, colours=palette, na.value = "green", guide = "colourbar")
 } else {
   p <- p + geom_polygon(aes(x=x, y=y, group=group, fill=signal), data=rotated_data)
 }