mbk0asis

library(ggplot2)
All <- read.csv("~/00-NGS/RNAseq/bov/niceM/Sham_Corrected/TopHat_UMD3.1_NCBI/log10_log2_mean.csv")
colnames(All) = c("chr","MI","MN","FI","FN",
                  "log10_MN_MI","log10_FI_MI","log10_FN_MI",
                  "log2_MN_MI","log2_FI_MI","log2_FN_MI")
head(All)

# set chr in natural order
All$chr <- factor(All$chr, 
                  levels=c("1","2","3","4","5","6","7","8","9","10",

mbk0asis

# gather "accepted_hits.bam" to one directory
$ find . -name "accepted_hits.bam" > bam_list
$ while read line; do cp $line  $(dirname $line).bam  ; done < bam_list


# rename bam files to shorten the names (e.g. SAMPLE.trim.cut.fq.gz.bam --> SAMPLE.bam)
$ rename 's/trim.cut.fq.gz.//g' *

mbk0asis

library(ggplot2)
library(ggpmisc)

p <- ggplot(df2,aes(log2(df2$high_mean),log2(df2$low_mean)), 
            xlab="log2(Setdb1_high)", ylab="log2(Setdb1_low)")

p + xlim(0,10) + ylim(0,10)+ theme_bw() + 
  geom_point(size=1,alpha=.3,col="black") +
  stat_density2d(aes(fill=..level..,alpha=..level..),geom='polygon',colour='grey50',bins=10, show.legend = F) + 
  scale_fill_continuous(low="yellow",high="red") +