Commit f42ccc86 authored by Valentina Galata's avatar Valentina Galata
Browse files

figures: added mash fig

parent 9c56a9ac
......@@ -26,8 +26,9 @@ workdir:
rule all:
input:
fig_mappability=["figures/fig_mappability.pdf","figures/fig_mappability_gdb_metat.pdf"],
fig_mappability=["figures/fig_mappability.pdf","figures/fig_mappability_gdb_metat.pdf"],
fig_quast="figures/fig_quast.pdf",
fig_mash="figures/fig_mash.pdf",
fig_gdb_rgi_aro3004454_flye="figures/fig_gdb_rgi_aro3004454_flye.pdf"
rule fig_mappability:
......@@ -68,6 +69,24 @@ rule fig_quast:
script:
os.path.join(SRC_DIR, "fig_quast.R")
rule fig_mash:
input:
zymo=os.path.join(config["samples"]["zymo"], "analysis/mash/contigs.dist"),
nwc=os.path.join(config["samples"]["nwc"], "analysis/mash/contigs.dist"),
gdb=os.path.join(config["samples"]["gdb"], "analysis/mash/contigs.dist"),
rumen=os.path.join(config["samples"]["rumen"], "analysis/mash/contigs.dist")
output:
pdf="figures/fig_mash.pdf"
log:
"figures/fig_mash.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_mash.R")
rule fig_gdb_rgi_aro3004454_flye_metaT:
input:
os.path.join(config["samples"]["gdb"], "mapping/metat/lr/flye/ASSEMBLY.POLISHED.sr.cov.perbase")
......
#!/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()
HCLUST <- list()
for(sname in names(snakemake@config$samples)){
testit::assert(sname %in% names(snakemake@input))
TABS[[sname]] <- read_mash_dist_asm(snakemake@input[[sname]])
HCLUST[[sname]] <- hclust(d=as.dist(TABS[[sname]]), method="complete")
}
############################## PLOT
# individual plots
FIGS <- list()
for(sname in names(snakemake@config$samples)){
FIGS[[sname]] <- as.ggplot(
pheatmap(
TABS[[sname]],
color=viridis(20),
border_color="white",
scale="none",
cluster_rows=HCLUST[[sname]],
cluster_cols=HCLUST[[sname]],
display_numbers=TRUE, number_color="black", number_format="%.3f", fontsize_number=12,
silent=TRUE
)
) +
labs(
title=LETTERS[which(names(TABS) == sname)],
subtitle=SAMPLE_NAMES[sname]
)
}
# combine plots
FIGS_ALL <- Reduce("+", FIGS) + plot_layout(ncol=2)
# PDF
pdf(snakemake@output$pdf, width=20, height=20)
print(FIGS_ALL)
dev.off()
\ No newline at end of file
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