mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 03:40:25 +08:00
31 lines
1.1 KiB
R
31 lines
1.1 KiB
R
#The purpose of this script is to make a simple jellyfish plot from a dataset like the one
|
|
#produced by the CUB.py script, also in the Github Utilities folder. This script was written
|
|
#by Auden Cote-L'Heureux and last updated in May 2023
|
|
|
|
library(tidyverse)
|
|
|
|
#Change this path
|
|
setwd('/Your/Working/Directory')
|
|
|
|
#You will need to change name of data frame below
|
|
#if you used the CUB.py script, it should be in the spreadsheets folder
|
|
#in the output and end in CompTrans.ENc.Raw.tsv
|
|
gc3 <- data.frame(read_tsv('CompTrans.ENc.Raw.tsv'))
|
|
|
|
gc3$GC3.Degen <- as.numeric(gc3$GC3.Degen)
|
|
gc3$ObsWrightENc_6Fold <- as.numeric(gc3$ObsWrightENc_6Fold)
|
|
|
|
#The data for the null expectation curve will be in the same folder as above
|
|
enc_null <- data.frame(read_tsv('ENc.Null.tsv'))
|
|
|
|
gc3_plot <- ggplot(data = gc3, mapping = aes(as.numeric(GC3.Degen), as.numeric(ObsWrightENc_6Fold))) +
|
|
geom_point() +
|
|
geom_line(data = enc_null, aes(GC3, ENc)) +
|
|
theme_classic() +
|
|
labs(x = '%GC at 3rd-pos 4-fold sites', y = 'Observed Wright ENc (6Fold)') +
|
|
theme(
|
|
legend.position = 'none'
|
|
)
|
|
|
|
gc3_plot
|