DRS_mapping_chrM.R
s-mitsutomi
2024-04-06
suppressPackageStartupMessages(library(tidyverse))## Warning: package 'ggplot2' was built under R version 4.2.3## Warning: package 'tidyr' was built under R version 4.2.3## Warning: package 'readr' was built under R version 4.2.3## Warning: package 'dplyr' was built under R version 4.2.3## Warning: package 'stringr' was built under R version 4.2.3devtools::load_all('~/Google Drive/My Drive/Scripts/R_packages/myUtilities/')## ℹ Loading myUtilitieslibrary(patchwork)## Warning: package 'patchwork' was built under R version 4.2.3Settings
data_dir <- '/Volumes/Mitsu_NGS_3/METTL2A/'
wd <- "/Users/s-mitsutomi/My Drive (shuheimitsutomi@ric.u-tokyo.ac.jp)/Analysis/METTL2A/"
setwd(wd)
figdir <- paste0(wd, 'Figures/DRS_mapping/')
tabledir <- paste0(wd, 'Tables/DRS/Mapping/Spliced/ChrM/')
theme_set(
theme_classic(base_size = 7) +
theme(legend.position = 'bottom')
)Functions
read_cpm_chrM <- function(path) {
read_tsv(path) |>
filter(seqname == 'chrM')
}Read data
chrM_cpms <-
fs::dir_ls(
path = paste0(wd, 'Tables/DRS/Mapping/Spliced/Bedgraph/CPM/'),
glob = '*.tsv.gz'
) |>
map(read_cpm_chrM) |>
purrr::reduce(bind_rows) |>
separate(sample, into = c('num', 'type', 'si', 'rep'), sep = '_')## Rows: 40611883 Columns: 6
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (3): seqname, sample, strand
## dbl (3): start, end, cpm
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 42480443 Columns: 6
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (3): seqname, sample, strand
## dbl (3): start, end, cpm
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.chrM_cpms## # A tibble: 168,455 × 9
## seqname start end cpm num type si rep strand
## <chr> <dbl> <dbl> <dbl> <chr> <chr> <chr> <chr> <chr>
## 1 chrM 0 1 -1000. 7 siMETTL2A I N1 -
## 2 chrM 1 2 -1008. 7 siMETTL2A I N1 -
## 3 chrM 2 3 -1023. 7 siMETTL2A I N1 -
## 4 chrM 3 4 -1031. 7 siMETTL2A I N1 -
## 5 chrM 4 7 -1036. 7 siMETTL2A I N1 -
## 6 chrM 7 8 -1039. 7 siMETTL2A I N1 -
## 7 chrM 8 9 -1054. 7 siMETTL2A I N1 -
## 8 chrM 9 11 -1058. 7 siMETTL2A I N1 -
## 9 chrM 11 12 -1054. 7 siMETTL2A I N1 -
## 10 chrM 12 13 -1055. 7 siMETTL2A I N1 -
## # ℹ 168,445 more rowsespresso_annotations <-
read_tsv(
paste0(wd, 'Tables/Espresso_AsPC1_annotation_cleaned_2024-03-29.tsv')
)## Rows: 36717 Columns: 14
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (12): seqname, source, feature, score, strand, frame, gene_id, transcrip...
## dbl (2): start, end
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.espresso_annotations## # A tibble: 36,717 × 14
## seqname source feature start end score strand frame gene_id transcript_id
## <chr> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr> <chr> <chr>
## 1 chr3 annot… transc… 3.15e6 3.15e6 . - . ENSG00… ENST00000498…
## 2 chr3 annot… transc… 3.15e6 3.15e6 . - . ENSG00… ENST00000459…
## 3 chr3 annot… transc… 3.15e6 3.18e6 . - . ENSG00… ENST00000231…
## 4 chr3 annot… transc… 3.15e6 3.18e6 . - . ENSG00… ENST00000432…
## 5 chr3 annot… transc… 3.13e6 3.13e6 . + . ENSG00… ENST00000339…
## 6 chr3 annot… transc… 3.15e6 3.16e6 . - . ENSG00… ENST00000488…
## 7 chr3 annot… transc… 3.13e6 3.13e6 . + . ENSG00… ENST00000420…
## 8 chr3 annot… transc… 3.14e6 3.15e6 . + . ENSG00… ENST00000698…
## 9 chr3 annot… transc… 3.17e6 3.18e6 . - . ENSG00… ENST00000450…
## 10 chr3 annot… transc… 3.15e6 3.15e6 . + . ENSG00… ENST00000698…
## # ℹ 36,707 more rows
## # ℹ 4 more variables: gene_type <chr>, gene_name <chr>, transcript_type <chr>,
## # transcript_name <chr>gencode_annotations <- read_gtf_transcripts(
'/Volumes/Mitsu_NGS_3/METTL2A/Database/gencode.v43.annotation_plus-tRNA.gtf'
)
gencode_annotations## # A tibble: 253,510 × 15
## seqname source feature start end score strand frame attributes gene_id
## <chr> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr> <noquote> <chr>
## 1 chrM ENSEMBL transcript 577 647 . + . gene_id "E… ENSG00…
## 2 chrM ENSEMBL transcript 648 1601 . + . gene_id "E… ENSG00…
## 3 chrM ENSEMBL transcript 1602 1670 . + . gene_id "E… ENSG00…
## 4 chrM ENSEMBL transcript 1671 3229 . + . gene_id "E… ENSG00…
## 5 chrM ENSEMBL transcript 3230 3304 . + . gene_id "E… ENSG00…
## 6 chrM ENSEMBL transcript 3230 3304 . + . gene_id "2… 26266
## 7 chrM ENSEMBL transcript 3307 4262 . + . gene_id "E… ENSG00…
## 8 chrM ENSEMBL transcript 4263 4331 . + . gene_id "E… ENSG00…
## 9 chrM ENSEMBL transcript 4329 4400 . - . gene_id "E… ENSG00…
## 10 chrM ENSEMBL transcript 4402 4469 . + . gene_id "E… ENSG00…
## # ℹ 253,500 more rows
## # ℹ 5 more variables: gene_type <chr>, gene_name <chr>, transcript_id <chr>,
## # transcript_type <chr>, transcript_name <chr>espresso_annotations_chrM <-
espresso_annotations |>
filter(seqname == 'chrM')
espresso_annotations_chrM## # A tibble: 23 × 14
## seqname source feature start end score strand frame gene_id transcript_id
## <chr> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr> <chr> <chr>
## 1 chrM novel_i… transc… 9222 13882 . - . <NA> ESPRESSO:chr…
## 2 chrM annotat… transc… 8366 8572 . + . ENSG00… ENST00000361…
## 3 chrM annotat… transc… 648 1601 . + . ENSG00… ENST00000389…
## 4 chrM annotat… transc… 14674 14742 . - . ENSG00… ENST00000387…
## 5 chrM annotat… transc… 14149 14673 . - . ENSG00… ENST00000361…
## 6 chrM annotat… transc… 1671 3229 . + . ENSG00… ENST00000387…
## 7 chrM annotat… transc… 3307 4262 . + . ENSG00… ENST00000361…
## 8 chrM annotat… transc… 7586 8269 . + . ENSG00… ENST00000361…
## 9 chrM annotat… transc… 10760 12137 . + . ENSG00… ENST00000361…
## 10 chrM annotat… transc… 14747 15887 . + . ENSG00… ENST00000361…
## # ℹ 13 more rows
## # ℹ 4 more variables: gene_type <chr>, gene_name <chr>, transcript_type <chr>,
## # transcript_name <chr>chrM_cpms |>
ggplot(aes(xmin = start, xmax = end, y = cpm, fill = si, group = si)) +
geom_rect(aes(ymin = 0, ymax = cpm), alpha = 1/4) +
facet_grid(rep ~ si) +
scale_y_continuous(breaks = seq(-20000, 80000, 20000)) 
mapping_chrM <-
chrM_cpms |>
ggplot(
aes(xmin = start, xmax = end, y = cpm, fill = si)) +
geom_rect(aes(ymin = 0, ymax = cpm)) +
facet_wrap( ~ num, ncol = 1) +
scale_y_continuous(breaks = seq(-20000, 80000, 20000)) +
scale_fill_manual(values = c('grey30', '#37d9cc', '#A3A3F9')) +
theme(legend.position = 'none')
annotation_chrM_barplot <-
gencode_annotations |>
#espresso_annotations_chrM |>
filter(seqname == 'chrM') |>
mutate(value = ifelse(strand == '+', 1, -1)) |>
ggplot(aes(xmin = start, xmax = end, y = value,
fill = gene_type)) +
scale_x_continuous(limits = c(0, max(chrM_cpms$end))) +
geom_rect(aes(ymin = 0, ymax = value)) +
scale_fill_manual(
values = c('gray30', '#F23E3E', 'gray30', '#3E3EF2')
)
chrM_plot <-
mapping_chrM + annotation_chrM_barplot +
plot_layout(ncol = 1, heights = c(19,1))
chrM_plot
ggsave(
filename = paste0(figdir, 'chrM_plot.pdf'), plot = chrM_plot,
width = 9, height = 18, units = 'cm')
chrM_cpms |>
filter(strand == '-') |>
ggplot(aes(xmin = start, xmax = end, y = cpm, fill = strand)) +
geom_rect(aes(ymin = 0, ymax = cpm)) +
facet_wrap( ~ si, ncol = 3) +
scale_y_continuous(limits = c(-500, 0)) +
theme_bw(base_size = 7)## Warning: Removed 3630 rows containing missing values or values outside the scale range
## (`geom_rect()`).
Sesison info
sessioninfo::session_info()## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.2.2 (2022-10-31)
## os macOS 14.4.1
## system aarch64, darwin20
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Asia/Tokyo
## date 2024-04-06
## pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
##
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## ! package * version date (UTC) lib source
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