Commit bb04dfe0 authored by Valentina Galata's avatar Valentina Galata
Browse files

figures: added rgi fig

parent fef8b5e4
......@@ -33,6 +33,7 @@ rule all:
fig_diamond_db="figures/fig_diamond_db.pdf",
fig_mmseqs2="figures/fig_mmseqs2.pdf",
fig_barrnap="figures/fig_barrnap.pdf",
fig_rgi=["figures/fig_rgi_counts.pdf", "figures/fig_rgi_overlap.pdf"],
fig_gdb_rgi_aro3004454_flye="figures/fig_gdb_rgi_aro3004454_flye.pdf"
rule fig_mappability:
......@@ -145,6 +146,25 @@ rule fig_barrnap:
script:
os.path.join(SRC_DIR, "fig_barrnap.R")
rule fig_rgi:
input:
zymo=os.path.join(config["samples"]["zymo"], "annotation/rgi/summary.tsv"),
nwc=os.path.join(config["samples"]["nwc"], "annotation/rgi/summary.tsv"),
gdb=os.path.join(config["samples"]["gdb"], "annotation/rgi/summary.tsv"),
rumen=os.path.join(config["samples"]["rumen"], "annotation/rgi/summary.tsv")
output:
pdf_c="figures/fig_rgi_counts.pdf",
pdf_o="figures/fig_rgi_overlap.pdf"
log:
"figures/fig_rgi.log"
params:
const=os.path.join(SRC_DIR, "const.R"),
utils=os.path.join(SRC_DIR, "utils.R")
conda:
os.path.join(ENV_DIR, "r.yaml")
script:
os.path.join(SRC_DIR, "fig_rgi.R")
rule fig_mmseqs2:
input:
zymo=os.path.join(config["samples"]["zymo"], "analysis/mmseqs2/summary.tsv"),
......
#!/usr/bin/Rscript
# Figure: QUAST statistics
############################## LOG
sink(file=file(snakemake@log[[1]], open="wt"), type=c("output", "message"))
############################## LIBS
suppressMessages(library(testit)) # assertions
suppressMessages(library(dplyr)) # tables
suppressMessages(library(patchwork)) # combine plots
suppressMessages(library(ggplotify)) # for as.ggplot
# custom
source(snakemake@params$const)
source(snakemake@params$utils)
############################## CONFIG
# assemblers
ASM_NAMES_CONFIG <- c(
snakemake@config$assemblers$lr,
snakemake@config$assemblers$sr,
snakemake@config$assemblers$hy
)
ASM_TOOL_NAMES <- ASM_TOOL_NAMES[ASM_NAMES_CONFIG]
ASM_TOOL_COLORS <- ASM_TOOL_COLORS[ASM_NAMES_CONFIG]; names(ASM_TOOL_COLORS) <- ASM_TOOL_NAMES[names(ASM_TOOL_COLORS)]
ASM_TOOL_SHAPES <- ASM_TOOL_SHAPES[ASM_NAMES_CONFIG]; names(ASM_TOOL_SHAPES) <- ASM_TOOL_NAMES[names(ASM_TOOL_SHAPES)]
############################## DATA
# individual tables
TABS <- list()
for(sname in names(snakemake@config$samples)){
testit::assert(sname %in% names(snakemake@input))
TABS[[sname]] <- read_rgi(snakemake@input[[sname]])
}
############################## PLOT
# individual plots
FIGS_c <- list()
FIGS_o <- list()
for(sname in names(snakemake@config$samples)){
if(nrow(TABS[[sname]]) > 0){
FIGS_c[[sname]] <-
plot_rgi_counts_total(proc_rgi(TABS[[sname]])$aggr) +
labs(
title=LETTERS[which(names(TABS) == sname)],
subtitle=SAMPLE_NAMES[sname]
)
FIGS_o[[sname]] <-
as.ggplot(plot_rgi_overlap(TABS[[sname]], "strict", "ARO")) +
labs(
title=LETTERS[which(names(TABS) == sname)],
subtitle=SAMPLE_NAMES[sname]
)
}
}
# combine plots
FIGS_ALL_c <- Reduce("+", FIGS_c) + plot_layout(ncol=2)
FIGS_ALL_o <- Reduce("+", FIGS_o) + plot_layout(ncol=2)
# PDF
pdf(snakemake@output$pdf_c, width=20, height=14)
print(FIGS_ALL_c)
dev.off()
pdf(snakemake@output$pdf_o, width=20, height=14)
print(FIGS_ALL_o)
dev.off()
\ No newline at end of file
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