From e63bce757d43868d1072c4c8e9d62b93e9bc8e6f Mon Sep 17 00:00:00 2001
From: james94 <james94@mi.fu-berlin.de>
Date: Thu, 11 Mar 2021 14:39:33 +0100
Subject: [PATCH] fix X11 display error
---
envs/merylMerq.yaml | 1 +
programs/merqury-1.1/plot/plot_spectra_cn.R | 12 +++++-------
2 files changed, 6 insertions(+), 7 deletions(-)
diff --git a/envs/merylMerq.yaml b/envs/merylMerq.yaml
index 96c6aed..d4f79ed 100644
--- a/envs/merylMerq.yaml
+++ b/envs/merylMerq.yaml
@@ -5,6 +5,7 @@ dependencies:
- igvtools
- openjdk=11.0.8
- r-base=3.6.3
+ - cairo=1.16.0
- r-ggplot2
- r-argparse
- r-scales
diff --git a/programs/merqury-1.1/plot/plot_spectra_cn.R b/programs/merqury-1.1/plot/plot_spectra_cn.R
index 2dd4757..f7153e3 100755
--- a/programs/merqury-1.1/plot/plot_spectra_cn.R
+++ b/programs/merqury-1.1/plot/plot_spectra_cn.R
@@ -133,14 +133,14 @@ plot_stack <- function(dat, name, x_max, y_max, zero, cutoff) {
}
save_plot <- function(name, type, outformat, h, w) {
- ggsave(file = paste(name, type, outformat, sep = "."), height = h, width = w)
+ ggsave(file = paste(name, type, outformat, sep = "."), type = c("cairo", "cairo-png", "Xlib", "quartz"), height = h, width = w)
}
spectra_cn_plot <- function(hist, name, zero="", cutoff="", w=6, h=4.5, x_max, y_max, type="all", pdf=FALSE) {
# Read hist
dat=read.table(hist, header=TRUE)
dat[,1]=factor(dat[,1], levels=unique(dat[,1]), ordered=TRUE) # Lock in the order
-
+
# Read asm-only
dat_0 = NULL
if (zero != "") {
@@ -180,19 +180,19 @@ spectra_cn_plot <- function(hist, name, zero="", cutoff="", w=6, h=4.5, x_max,
if (pdf) {
outformat="pdf"
}
-
+
if (type == "all" || type == "line") {
print("## Line graph")
plot_line(dat, name, x_max, y_max, zero = dat_0, cutoff = dat_cut)
save_plot(name=name, type="ln", outformat, h=h, w=w)
}
-
+
if (type == "all" || type == "fill") {
print("## Area under the curve filled")
plot_fill(dat, name, x_max, y_max, zero = dat_0, cutoff = dat_cut)
save_plot(name=name, type="fl", outformat, h=h, w=w)
}
-
+
if (type == "all" || type == "stack") {
print("## Stacked")
plot_stack(dat, name, x_max, y_max, zero = dat_0, cutoff = dat_cut)
@@ -201,5 +201,3 @@ spectra_cn_plot <- function(hist, name, zero="", cutoff="", w=6, h=4.5, x_max,
}
spectra_cn_plot(hist = args$file, name = args$output, zero = args$zero, cutoff = args$cutoff, h = args$ydim, w = args$xdim, x_max = args$xmax, y_max = args$ymax, type = args$type, pdf = args$pdf)
-
-
--
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