From 1c0e4099c5d79a0ec4813c3465ea7c2c4938cc7c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 13 Jun 2023 15:31:28 +0200
Subject: [PATCH] fix kmer_merge to kmer_plot connection
---
src/bin/kmerclust_merge.R | 3 ++-
src/bin/kmerclust_plot.R | 7 ++++---
src/main.nf | 4 ++--
3 files changed, 8 insertions(+), 6 deletions(-)
diff --git a/src/bin/kmerclust_merge.R b/src/bin/kmerclust_merge.R
index cadf100..675b3da 100644
--- a/src/bin/kmerclust_merge.R
+++ b/src/bin/kmerclust_merge.R
@@ -3,10 +3,11 @@ library(kmerclust)
args <- commandArgs(trailingOnly = TRUE)
print(args)
res_files <- list.files(pattern = "Rdata$")
+print(res_files)
res_total <- NULL
for (res_file in res_files) {
load(res_file)
res_total <- rbind(res_total, res)
}
res <- res_total
-save(res, file = paste0(args[1], "_boot", ".Rdata"))
+save(res, file = paste0(args[1], "_boot.Rdata"))
diff --git a/src/bin/kmerclust_plot.R b/src/bin/kmerclust_plot.R
index 42d1aab..9f7bca8 100644
--- a/src/bin/kmerclust_plot.R
+++ b/src/bin/kmerclust_plot.R
@@ -6,17 +6,18 @@ print(args)
load(file = paste0(args[1], ".Rdata"))
load(file = paste0(args[1], "_boot.Rdata"))
+print(res)
res %>%
ggplot(aes(x = name, y = BIC)) +
- geom_violin() %>%
+ geom_violin() +
theme_bw()
ggsave(paste0(args[1], "_BIC.pdf"))
res %>%
ggplot(aes(x = name, y = WSS_f / BSS)) +
- geom_violin() %>%
+ geom_violin() +
theme_bw()
ggsave(paste0(args[1], "_WSS_BSS.pdf"))
count %>%
- ggplot(aes(x = count_m, y = count_f)) %>%
+ ggplot(aes(x = count_m, y = count_f)) +
theme_bw()
ggsave(paste0(args[1], "_scatter.pdf"))
diff --git a/src/main.nf b/src/main.nf
index 423c4d3..174ca75 100644
--- a/src/main.nf
+++ b/src/main.nf
@@ -33,6 +33,6 @@ workflow {
COLLATEKMER(MERGEKMER.out.csv.map{it -> [it[0].specie, it[1]] }.groupTuple())
KMERCLUST_LOAD(COLLATEKMER.out.csv, params_csv.collect())
KMERCLUST(Channel.of(1..params.bootstrap).combine(KMERCLUST_LOAD.out.rdata))
- KMERCLUST_MERGE(KMERCLUST.out.rdata.map{it -> [it[1], it[2]]}.groupTuple())
- KMERCLUST_PLOT(KMERCLUST_MERGE.out.rdata)
+ KMERCLUST_MERGE(KMERCLUST.out.rdata.groupTuple())
+ KMERCLUST_PLOT(KMERCLUST_MERGE.out.rdata.mix(KMERCLUST_LOAD.out.rdata).groupTuple())
}
--
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