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ORFweights.r
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########################################################################################
## This file is a part of YAP package of scripts. https://github.com/shpakoo/YAP
## Distributed under the MIT license: http://www.opensource.org/licenses/mit-license.php
## Copyright (c) 2011-2013 Sebastian Szpakowski
########################################################################################
library(ggplot2)
library(grid)
library(scales)
multiplot <- function(..., plotlist=NULL, cols=1, layout=NULL)
{
require(grid)
# Make a list from the ... arguments and plotlist
plots <- c(list(...), plotlist)
numPlots = length(plots)
# If layout is NULL, then use 'cols' to determine layout
if (is.null(layout))
{
layout = grid.layout(ceiling(numPlots/cols), cols)
}
# create a panel that will be used to map ids later
panel = matrix(1:(layout$nrow * layout$ncol), nrow = layout$nrow, ncol = layout$ncol, byrow=TRUE )
if (numPlots==1)
{
print(plots[[1]])
}
else
{
# Set up the page
grid.newpage()
pushViewport(viewport(layout = layout))
for (i in 1:numPlots)
{
matching <- as.data.frame(which(panel == i, arr.ind = TRUE))
print ( plots[[i]], vp = viewport( layout.pos.row = matching$row,
layout.pos.col = matching$col)
)
}
}
}
loadWeights <- function ()
{
x = data.frame()
for (file in dir (pattern= glob2rx("*.weight")))
{
newfile = unlist(strsplit(file, "\\."))
newfile = newfile[-length(newfile)]
newfile = paste(paste(newfile, collapse=".", sep=""), "normweight", sep= ".")
print (newfile)
tmp = read.table(file, sep="\t", header = FALSE)
names(tmp)<-c("orfid", "coverage")
tmp$scaled = tmp$coverage / median(tmp$coverage)
tmp$scaledlog2 = log2(tmp$coverage / median(tmp$coverage))
###
write.table(tmp, newfile, sep="\t", row.names=FALSE, col.names=TRUE, quote=FALSE)
###
tmp$file = rep(file, nrow(tmp))
cat(file, median(tmp$coverage), mean(tmp$coverage), "\n", sep= "\t")
if (nrow(x)==0)
{
x = tmp
}
else
{
x = rbind(tmp, x)
}
}
return (x)
}
################################################################################
global = loadWeights()
files = unique(global$file)
####### transforms
y_trans_log10 = scale_y_log10( breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x)))
x_trans_log10 = scale_x_log10( breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x)))
y_trans_log2 = scale_y_log10( breaks = trans_breaks("log2", function(x) 2^x),
labels = trans_format("log2", math_format(2^.x)))
x_trans_log2 = scale_x_log10( breaks = trans_breaks("log2", function(x) 2^x),
labels = trans_format("log2", math_format(2^.x)))
####### plots
A1 = (ggplot(global, aes(file, coverage, color=file))
+ geom_boxplot()
+ coord_flip()
+ theme(axis.ticks = element_blank(), axis.text.y = element_blank())
)
A2 = (ggplot(global, aes(file, scaled, color=file))
+ geom_boxplot()
+ coord_flip()
+ theme(axis.ticks = element_blank(), axis.text.y = element_blank())
)
A3 = (ggplot(global, aes(file, scaledlog2, color=file))
+ geom_boxplot()
+ coord_flip()
+ theme(axis.ticks = element_blank(), axis.text.y = element_blank())
)
B1 = (ggplot(global, aes(coverage, ..count.., fill=file, group=file ))
+ stat_bin(aes(y=..count..), geom="area", position="stack", weight=2)
)
B2 = (ggplot(global, aes(scaled, ..count.., fill=file, group=file ))
+ stat_bin(aes(y=..count..), geom="area", position="stack", weight=2)
)
B3 = (ggplot(global, aes(scaledlog2, ..count.., fill=file, group=file ))
+ stat_bin(aes(y=..count..), geom="area", position="stack", weight=2)
)
C1 = (ggplot(global, aes(coverage, ..count.., fill=file, group=file ))
+ stat_bin(aes(y=..count..), geom="area", position="dodge", alpha=0.5, weight=2)
)
C2 = (ggplot(global, aes(scaled, ..count.., fill=file, group=file ))
+ stat_bin(aes(y=..count..), geom="area", position="dodge", alpha=0.5, weight=2)
)
C3 = (ggplot(global, aes(scaledlog2, ..count.., fill=file, group=file ))
+ stat_bin(aes(y=..count..), geom="area", position="dodge", alpha=0.5, weight=2)
)
D1 = (ggplot(global, aes(coverage, fill=file, group=file ))
+ geom_bar(position="fill")
)
D2 = (ggplot(global, aes(scaled, fill=file, group=file ))
+ geom_bar(position="fill")
)
D3 = (ggplot(global, aes(scaledlog2, fill=file, group=file ))
+ geom_bar(position="fill")
)
################ rendered output files
png("COVERAGE_GG.png", width=30, height = 2 + 4 * length(files), units="in", res=250)
multiplot( A1, A2, A3,
B1, B2, B3,
C1, C2, C3,
D1, D2, D3,
cols=3
)
dev.off()
png("COVERAGE_log10counts_GG.png", width=30, height = 2 + 4 * length(files), units="in", res=250)
multiplot( A1 + y_trans_log10, A2 + y_trans_log10, A2 + y_trans_log10,
B1 + y_trans_log10, B2 + y_trans_log10, B2 + y_trans_log10,
C1 + y_trans_log10, C2 + y_trans_log10, C2 + y_trans_log10,
D1 + y_trans_log10, D2 + y_trans_log10, D2 + y_trans_log10,
cols=3
)
dev.off()
png("COVERAGE_facet_GG.png", width=10, height = 2 + 2 * (4 * length(files)), units="in", res=250)
multiplot(
B1 + facet_grid( file ~ .) , B2 + facet_grid( file ~ .), B3 + facet_grid( file ~ .) ,
cols=1
)
dev.off()
png("COVERAGE_log10counts_facet_GG.png", width=10, height = 2 + 2 * (4 * length(files)), units="in", res=250)
multiplot(
B1 + y_trans_log10 + facet_grid( file ~ .) , B2 + y_trans_log10 + facet_grid( file ~ .), B3 + y_trans_log10 + facet_grid( file ~ .),
cols=1
)
dev.off()