Skip to content

Adding a script for generating box plots using rseqc inferExperiment #15

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
MobasharAhmad wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Adding a script for generating box plots using rseqc inferExperiment #15

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
53 changes: 53 additions & 0 deletions Manuscript_Code/NBISC100_project/thymus/rseqc_metrics/thymus_RseQC_inferExperiment_mobashar
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,53 @@
#load library
library(ggplot2)
library(tidyverse)
library(scales)
library(RColorBrewer)

#load data
thymus.metrics.df <- read_csv("thymus_FLT_GC_qc_metrics.csv")

# prepare data for RseQC infer experiment
RseQC_inferExp.thymus.metrics.df <-thymus.metrics.df %>%
select(osd_num, pct_sense)

# Add a new column for library kit
RseQC_inferExp.thymus.metrics.df <- RseQC_inferExp.thymus.metrics.df %>%
mutate(library_kit= recode(osd_num,
"OSD-244"="ribo-deplete kit",
"OSD-289"="ribo-deplete kit",
"OSD-421"="polyA-UPX kit",
"OSD-515"="ribo-deplete kit",
"OSD-457"="ribo-deplete kit"))

# Box_plot1: thymus_RseQC_strandedness_individual_datasets

ggplot(RseQC_inferExp.thymus.metrics.df, aes(x = osd_num, y = pct_sense, fill = osd_num)) +
geom_boxplot(size = 0.1, varwidth = TRUE) +
stat_boxplot(geom = "errorbar", width = 0.2, size= 0.1)+
scale_y_continuous(breaks = pretty_breaks(n = 10))+
scale_fill_brewer(palette = "Set2")+
labs(title = "Strandedness of Individual Thymus Datasets", x = "OSD-number", y = "sense(%)") +
theme_classic() +
theme(legend.position = "none")+
theme(plot.title = element_text(hjust = 0.5))

ggsave("RseQC_strandedness_thymus_indivisual_datasets_MA.png", dpi = 300,
width = 6.7, height = 4, units = "in")


# Box_plot2: thymus_RseQC_strandedness by library kit
ggplot(RseQC_inferExp.thymus.metrics.df, aes(x = osd_num, y = pct_sense, fill = osd_num)) +
geom_boxplot(size = 0.1, varwidth = TRUE) +
stat_boxplot(geom = "errorbar", width = 0.2, size= 0.1)+
facet_wrap(~library_kit, scales = "free_x", drop = TRUE)+
scale_y_continuous(breaks = pretty_breaks(n = 10))+
scale_fill_brewer(palette = "Set2") +
labs(title = "Strandedness of Thymus Datasets by Library Kits", x = "OSD-number", y = "sense(%)") +
theme_classic() +
theme(legend.position = "none")+
theme(plot.title = element_text(hjust = 0.5))

ggsave("RseQC_strandedned_thymus_libraryKits_MA.png", dpi = 300,
width = 6.7, height = 4, units = "in")