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Adding a script for generating box plots using rseqc read distribution metrics #16

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180 changes: 180 additions & 0 deletions ...script_Code/NBISC100_project/thymus/rseqc_metrics/thymus_RseQC_read_distribution_mobashar
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#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 read distributions
RseQC_read_distribution.thymus.metrics.df <-thymus.metrics.df %>%
select(osd_num, cds_exons_pct,`5_utr_exons_pct`,`3_utr_exons_pct`,introns_pct, tss_up_5kb_10kb_pct)

# Add a new column for library kit
RseQC_read_distribution.thymus.metrics.df <- RseQC_read_distribution.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_cds_exons_individual_datasets
ggplot(RseQC_read_distribution.thymus.metrics.df, aes(x = osd_num, y = cds_exons_pct, 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 = "Read Distribution (CDS Exons) of Individual Thymus Datasets", x = "OSD-number", y = "cds exons(%)") +
theme_classic() +
theme(legend.position = "none")+
theme(plot.title = element_text(hjust = 0.5))

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


# Box_plot2: thymus_RseQC_cds_exons by library kit
ggplot(RseQC_read_distribution.thymus.metrics.df, aes(x = osd_num, y = cds_exons_pct, 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 = "Read Distribution (CDS Exons) of Thymus Datasets by Library Kits", x = "OSD-number", y = "cds exons(%)") +
theme_classic() +
theme(legend.position = "none")+
theme(plot.title = element_text(hjust = 0.5))

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



## 5'UTRs---------------
# Box_plot1: thymus_RseQC_5'UTRs_individual_datasets
ggplot(RseQC_read_distribution.thymus.metrics.df, aes(x = osd_num, y = `5_utr_exons_pct`, 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 = "Read Distribution (5' UTRs) of Individual Thymus Datasets", x = "OSD-number", y = "5' UTRs (%)") +
theme_classic() +
theme(legend.position = "none")+
theme(plot.title = element_text(hjust = 0.5))

ggsave("RseQC_5UTRs_thymus_indivisual_datasets_MA.png", dpi = 300,
width = 6.7, height = 4, units = "in")


# Box_plot2: thymus_RseQC_5'UTR by library kit
ggplot(RseQC_read_distribution.thymus.metrics.df, aes(x = osd_num, y = `5_utr_exons_pct`, 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 = "Read Distribution (5' UTRs) of Thymus Datasets by Library Kits", x = "OSD-number", y = "5' UTRs (%)") +
theme_classic() +
theme(legend.position = "none")+
theme(plot.title = element_text(hjust = 0.5))

ggsave("RseQC_5UTRs_thymus_libraryKits_MA.png", dpi = 300,
width = 6.7, height = 4, units = "in")

## 3' UTRs --------------
# Box_plot1: thymus_RseQC_3'UTRs_individual_datasets
ggplot(RseQC_read_distribution.thymus.metrics.df, aes(x = osd_num, y = `3_utr_exons_pct`, 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 = "Read Distribution (3' UTRs) of Individual Thymus Datasets", x = "OSD-number", y = "3' UTRs (%)") +
theme_classic() +
theme(legend.position = "none")+
theme(plot.title = element_text(hjust = 0.5))

ggsave("RseQC_3UTRs_thymus_indivisual_datasets_MA.png", dpi = 300,
width = 6.7, height = 4, units = "in")


# Box_plot2: thymus_RseQC_3'UTR by library kit
ggplot(RseQC_read_distribution.thymus.metrics.df, aes(x = osd_num, y = `3_utr_exons_pct`, 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 = "Read Distribution (3' UTRs) of Thymus Datasets by Library Kits", x = "OSD-number", y = "3' UTRs (%)") +
theme_classic() +
theme(legend.position = "none")+
theme(plot.title = element_text(hjust = 0.5))

ggsave("RseQC_3UTRs_thymus_libraryKits_MA.png", dpi = 300,
width = 6.7, height = 4, units = "in")


## introns ------------
# Box_plot1: thymus_RseQC_introns_individual_datasets
ggplot(RseQC_read_distribution.thymus.metrics.df, aes(x = osd_num, y = introns_pct, 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 = "Read Distribution (Introns) of Individual Thymus Datasets", x = "OSD-number", y = "introns (%)") +
theme_classic() +
theme(legend.position = "none")+
theme(plot.title = element_text(hjust = 0.5))

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


# Box_plot2: thymus_RseQC_3'UTR by library kit
ggplot(RseQC_read_distribution.thymus.metrics.df, aes(x = osd_num, y = introns_pct, 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 = "Read Distribution (Introns) of Thymus Datasets by Library Kits", x = "OSD-number", y = "introns (%)") +
theme_classic() +
theme(legend.position = "none")+
theme(plot.title = element_text(hjust = 0.5))

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

## tss_up 5 to 10 kb -------
# Box_plot1: thymus_RseQC_tss_up5-10_individual_datasets
ggplot(RseQC_read_distribution.thymus.metrics.df, aes(x = osd_num, y = tss_up_5kb_10kb_pct, 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 = "Read Distribution (TSS up 5-10 kb) of Individual thymus Datasets", x = "OSD-number", y = "tss up 5-10 kb (%)") +
theme_classic() +
theme(legend.position = "none")+
theme(plot.title = element_text(hjust = 0.5))

ggsave("RseQC_tssUp5-10_thymus_indivisual_datasets_MA.png", dpi = 300,
width = 6.7, height = 4, units = "in")


# Box_plot2: thymus_RseQC_introns by library kit
ggplot(RseQC_read_distribution.thymus.metrics.df, aes(x = osd_num, y = tss_up_5kb_10kb_pct, 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 = "Read Distribution (TSS up 5-10 kb) of Thymus Datasets by Library Kits", x = "OSD-number", y = "tss up 5-10 kb (%)") +
theme_classic() +
theme(legend.position = "none")+
theme(plot.title = element_text(hjust = 0.5))

ggsave("RseQC_tssUp5_thymus_libraryKits_MA.png", dpi = 300,
width = 6.7, height = 4, units = "in")