Mercurial > repos > artbio > small_rna_map
changeset 2:7feee0446c5c draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 339b809565195d32271f5d17c689dee15063e477
| author | artbio |
|---|---|
| date | Wed, 12 Jul 2017 13:40:36 -0400 |
| parents | 2299eb1e7c93 |
| children | 2e0dc6032a98 |
| files | small_rna_map.r small_rna_map.xml test-data/output.pdf |
| diffstat | 3 files changed, 12 insertions(+), 88 deletions(-) [+] |
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--- a/small_rna_map.r Tue Jul 11 09:01:19 2017 -0400 +++ b/small_rna_map.r Wed Jul 12 13:40:36 2017 -0400 @@ -25,18 +25,8 @@ #Make initial figures p <- ggplot(Table, aes(x=Coordinate, y=Nbr_reads, colour=Polarity)) + colScale+ - geom_segment(aes(y = 0, - x = Coordinate, - yend = Nbr_reads, - xend = Coordinate, - color=Polarity), - alpha=1 - ) + - geom_segment(aes(y = Nbr_reads, - x = 0, - yend=Nbr_reads, - xend=Chrom_length), alpha=0 - )+ + geom_segment(aes(y = 0, x = Coordinate, yend = Nbr_reads, xend = Coordinate, color=Polarity), alpha=1) + + geom_segment(aes(y = Nbr_reads, x = 0, yend=Nbr_reads, xend=Chrom_length), alpha=0)+ facet_wrap(Dataset~Chromosome, scales="free", nrow=1, labeller = label_wrap_gen(multi_line = FALSE))+ scale_y_continuous(breaks = function(x) round(pretty(seq(-(max(x) + 1), (max(x) + 1)))))+#to display only integer values on y axis geom_hline(yintercept=0, size=0.3)+ @@ -51,29 +41,25 @@ mylegend <- legendGrob(c("F", "R", "Median", "Mean"), pch=22, gp=gpar(col = c("red","blue","black","yellow"), fill = c("red","blue","black","yellow"))) - # The second plot cols<- c("Median"="#000000", "Mean"="#fffa00") p2 <- ggplot(Table, aes(x = Coordinate, group=1)) + geom_point(aes(y=Median, colour="Median"), alpha=1, size = 1) + - geom_point(aes(y=Mean, colour="Mean"), alpha= 0.3, size = 1.2)+ + geom_point(aes(y=Mean, colour="Mean"), alpha= 0.5, size = 1.2)+ scale_colour_manual(name="", values=cols)+ expand_limits(y = seq(0,max(Table$Median),by=5)) + facet_wrap(Dataset~Chromosome, scales="free", nrow=1, labeller = label_wrap_gen(multi_line = FALSE))+ - geom_segment(aes(y = Nbr_reads, - x = 0, - yend=Nbr_reads, - xend=Chrom_length), alpha=0 - )+ - scale_y_continuous(limits = c(0,max(Table$Median)), position = "right")+ - theme(strip.text = element_text(size = 6, lineheight = 0.1), + geom_segment(aes(y = Nbr_reads, x = 0, yend=Nbr_reads, xend=Chrom_length), alpha=0)+ + scale_y_continuous(limits = c(0,max(Table$Median)), position = "left")+ + theme(strip.background = element_blank(), + strip.text.x = element_blank(), panel.background = element_rect(fill = NA), panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.border = element_rect(fill = NA, colour = "grey50"), axis.text = element_text(size = 6), - legend.position = "none" - ) + axis.title = element_blank(), + legend.position = "none") # Transforme ggplot graphs on list of graphs plot.list1 <- by(data = Table, @@ -90,70 +76,8 @@ p2 %+% x }) -# A function to get the original tick mark length -plot_theme <- function(p) { - plyr::defaults(p$theme, theme_get()) -} - -# ggplot contains many labels that are themselves complex grob; -# usually a text grob surrounded by margins. -# When moving the grobs from, say, the left to the right of a plot, -# Make sure the margins and the justifications are swapped around. -# The function below does the swapping. -# Taken from the cowplot package: -# https://github.com/wilkelab/cowplot/blob/master/R/switch_axis.R - -hinvert_title_grob <- function(grob){ - - # Swap the widths - widths <- grob$widths - grob$widths[1] <- widths[3] - grob$widths[3] <- widths[1] - grob$vp[[1]]$layout$widths[1] <- widths[3] - grob$vp[[1]]$layout$widths[3] <- widths[1] - - # Fix the justification - grob$children[[1]]$hjust <- 1 - grob$children[[1]]$hjust - grob$children[[1]]$vjust <- 1 - grob$children[[1]]$vjust - grob$children[[1]]$x <- unit(1, "npc") - grob$children[[1]]$x - grob -} - -dual_axis <- function(v1,v2){ -# Get the ggplot grobs - g1 <- ggplot_gtable(ggplot_build(v1)) - g2 <- ggplot_gtable(ggplot_build(v2)) -# Get the locations of the plot panels in g1. - pp <- c(subset(g1$layout, grepl("panel", g1$layout$name), se = t:r)) -# Overlap panels for second plot on those of the first plot - g <- gtable_add_grob(g1, g2$grobs[grepl("panel", g1$layout$name)], - pp$t, pp$l, pp$b, pp$l) -# Get the y axis from g2 (axis line, tick marks, and tick mark labels) - index <- which(g2$layout$name == "axis-r-1-1") # Which grob. - yaxis <- g2$grobs[[index]] # Extract the grob - ticks <- yaxis$children[[2]] # swap tick marks and tick mark labels - -# Move the tick marks, Tick mark lengths can change. - tml <- plot_theme(p)$axis.ticks.length # Tick mark length - ticks$grobs[[1]]$x <- ticks$grobs[[1]]$x - unit(1, "npc") + tml - -# Swap margins and fix justifications for the tick mark labels -ticks$grobs[[2]] <- hinvert_title_grob(ticks$grobs[[2]]) - -# Put ticks back into yaxis -yaxis$children[[2]] <- ticks - -# Put the transformed yaxis on the right side of g1 -g <- gtable_add_cols(g, g2$widths[g2$layout[index, ]$l], max(pp$r)) -g <- gtable_add_grob(g, yaxis, max(pp$t), max(pp$r) + 1, max(pp$b), max(pp$r) + 1, - clip = "off") - -} - -plots <- list() -len = length(plot.list1) -for(i in 1:len ) {plots[[i]] <- dual_axis(plot.list1[[i]],plot.list2[[i]])} # Plotting in multiple pages with different rows -multi.plot<-do.call(marrangeGrob,list(grobs=plots,ncol=1,nrow=8,top=NULL, bottom="Coordinates(nt)", left="Number of reads", right= mylegend)) +multi.plot<-do.call(marrangeGrob,list(grobs=rbind(plot.list1,plot.list2),ncol=1,nrow=8,top=NULL, + bottom="Coordinates(nt)", left="Number of reads / Median & Mean", right= mylegend)) ggsave(args$output_pdf, device="pdf", plot=multi.plot, height=11.69, width=8.2)
--- a/small_rna_map.xml Tue Jul 11 09:01:19 2017 -0400 +++ b/small_rna_map.xml Wed Jul 12 13:40:36 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="small_rna_map" name="small rna map" version="0.2.0"> +<tool id="small_rna_map" name="small rna map" version="0.3.0"> <description></description> <requirements> <requirement type="package" version="1.11.2=py27_0">numpy</requirement>