Load 'em
df <- read.csv("/data2/rnaseq/cyperus/assembly/transrate.csv")
df$default <- grepl(df$assembly, pattern = "def")
df$assembly <- gsub(df$assembly, pattern = "\\.scafSeq", replacement = "")
df$assembly <- gsub(df$assembly, pattern = "\\.def", replacement = "")
library(reshape2)
names(df)[1] <- "species"
df.m <- melt(df, id = c("species", "default"))
subset(df.m, variable == "rbh_per_reference")
## species default variable value
## 81 cd TRUE rbh_per_reference 0.2559
## 82 cd FALSE rbh_per_reference 0.2514
## 83 clg TRUE rbh_per_reference 0.2665
## 84 clg FALSE rbh_per_reference 0.2797
## 85 clv TRUE rbh_per_reference 0.2446
## 86 clv FALSE rbh_per_reference 0.2486
## 87 clz TRUE rbh_per_reference 0.2752
## 88 clz FALSE rbh_per_reference 0.2927
Plot 'em
library(ggplot2)
ggplot(df.m, aes(x = species, y = value, fill = default)) + geom_bar(stat = "identity",
position = "dodge") + facet_grid(variable ~ ., scales = "free")