From f45459a1eaa6c424e1cf86e7e38de51b5d967d81 Mon Sep 17 00:00:00 2001
From: Valentina Galata <valentina.galata@uni.lu>
Date: Tue, 18 Aug 2020 08:55:24 +0200
Subject: [PATCH] report: update to include new assemblers; fixed tool order in
cdhit/diamond plots
---
workflow_report/scripts/report.R | 9 +++++++--
workflow_report/scripts/utils.R | 25 +++++++++++++------------
2 files changed, 20 insertions(+), 14 deletions(-)
diff --git a/workflow_report/scripts/report.R b/workflow_report/scripts/report.R
index 1ba421d..93f677f 100644
--- a/workflow_report/scripts/report.R
+++ b/workflow_report/scripts/report.R
@@ -198,8 +198,10 @@ FIGS$prodigal$glength_density <-
# DIAMOND
if("diamond" %in% snakemake@config$steps_annotation){
- TABS$diamond <- read_diamond(snakemake@input$diamond[1])
- TABS$diamond_melted <- reshape2::melt(TABS$diamond, id.vars=c("tool"))
+ TABS$diamond <- read_diamond(snakemake@input$diamond[1])
+ TABS$diamond_melted <- reshape2::melt(TABS$diamond, id.vars=c("tool"))
+ TABS$diamond$tool <- factor(TABS$diamond$tool, ordered=TRUE, levels=ASM_TOOL_NAMES)
+ TABS$diamond_melted$tool <- factor(TABS$diamond_melted$tool, ordered=TRUE, levels=ASM_TOOL_NAMES)
FIGS$diamond <- list()
FIGS$diamond$violin <-
@@ -394,6 +396,9 @@ if("mash_dist" %in% snakemake@config$steps_analysis){
if("cdhit" %in% snakemake@config$steps_analysis){
TABS$cdhit <- read_cdhit(snakemake@input$cdhit[1])
+ TABS$cdhit$tool1 <- factor(TABS$cdhit$tool1, ordered=TRUE, levels=ASM_TOOL_NAMES)
+ TABS$cdhit$tool2 <- factor(TABS$cdhit$tool2, ordered=TRUE, levels=ASM_TOOL_NAMES)
+
FIGS$cdhit <-
ggplot(data=TABS$cdhit, aes(x=tool2, y=unique, fill=tool2)) +
geom_col() +
diff --git a/workflow_report/scripts/utils.R b/workflow_report/scripts/utils.R
index 7495368..5455787 100644
--- a/workflow_report/scripts/utils.R
+++ b/workflow_report/scripts/utils.R
@@ -395,7 +395,6 @@ DIAMOND_VAR_LABELLER <- function(x){
# names
ASM_TOOL_NAMES <- c(
- # LR, SR, hybrid
"flye"="Flye",
"wtdbg2"="wtdbg2",
"canu"="Canu",
@@ -405,25 +404,27 @@ ASM_TOOL_NAMES <- c(
"metaspadeshybrid"="metaSPAdes (H)",
"imp3"="IMP3 (MG/MT)"
)
+# select assemblers from config
ASM_TOOL_NAMES <- ASM_TOOL_NAMES[c(
snakemake@config$assemblers$lr,
snakemake@config$assemblers$sr,
- snakemake@config$assemblers$hy
+ snakemake@config$assemblers$hy,
+ snakemake@config$assemblers$hyhy
)]
# colors
-ASM_TOOL_PALETTE1 <- ggsci::pal_nejm("default", alpha=1)(7)
-ASM_TOOL_PALETTE2 <- ggsci::pal_nejm("default", alpha=0.8)(7)
-ASM_TOOL_PALETTE3 <- ggsci::pal_nejm("default", alpha=0.6)(7)
-ASM_TOOL_PALETTE4 <- ggsci::pal_nejm("default", alpha=0.4)(7)
+ASM_TOOL_PALETTE1 <- ggsci::pal_nejm("default", alpha=1)(8)
+ASM_TOOL_PALETTE2 <- ggsci::pal_nejm("default", alpha=0.8)(8)
+ASM_TOOL_PALETTE3 <- ggsci::pal_nejm("default", alpha=0.6)(8)
+ASM_TOOL_PALETTE4 <- ggsci::pal_nejm("default", alpha=0.4)(8)
ASM_TOOL_COLORS <- c(
- # LR, SR, hybrid
"Flye"=ASM_TOOL_PALETTE1[1],
"wtdbg2"=ASM_TOOL_PALETTE1[2],
- "MEGAHIT"=ASM_TOOL_PALETTE1[3],
- "metaSPAdes"=ASM_TOOL_PALETTE1[4],
- "OPERA-MS"=ASM_TOOL_PALETTE1[5],
- "metaSPAdes (H)"=ASM_TOOL_PALETTE1[6],
- "IMP3 (MG/MT)"=ASM_TOOL_PALETTE1[7]
+ "Canu"=ASM_TOOL_PALETTE1[3],
+ "MEGAHIT"=ASM_TOOL_PALETTE1[4],
+ "metaSPAdes"=ASM_TOOL_PALETTE1[5],
+ "OPERA-MS"=ASM_TOOL_PALETTE1[6],
+ "metaSPAdes (H)"=ASM_TOOL_PALETTE1[7],
+ "IMP3 (MG/MT)"=ASM_TOOL_PALETTE1[8]
)
ASM_TOOL_COLORS <- ASM_TOOL_COLORS[ASM_TOOL_NAMES]
--
GitLab