From 5fff23d36b2960b9876699145768fbf1b573a4bd Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Wed, 22 Jun 2022 10:26:50 +0200
Subject: [PATCH] src/03_ERCC_analysis_code.R: cosmetic changes
---
src/03_ERCC_analysis_code.R | 24 ++++++++++++++++++------
1 file changed, 18 insertions(+), 6 deletions(-)
diff --git a/src/03_ERCC_analysis_code.R b/src/03_ERCC_analysis_code.R
index e0fae81..d819d0d 100644
--- a/src/03_ERCC_analysis_code.R
+++ b/src/03_ERCC_analysis_code.R
@@ -17,7 +17,10 @@ ercc_count_matrix <- get_count_matrix(
0
)[, colnames(data_count_matrix)]
-data_count_matrix <- data.frame(gene = rownames(data_count_matrix), data_count_matrix)
+data_count_matrix <- data.frame(
+ gene = rownames(data_count_matrix),
+ data_count_matrix
+)
dir.create("./results/matrice_count/")
write.table(data_count_matrix,
file = "./results/matrice_count/coding_gene_matrices.txt",
@@ -26,7 +29,10 @@ write.table(data_count_matrix,
row.names = F
)
-ercc_count_matrix_new <- data.frame(gene = rownames(ercc_count_matrix), ercc_count_matrix)
+ercc_count_matrix_new <- data.frame(
+ gene = rownames(ercc_count_matrix),
+ ercc_count_matrix
+)
write.table(ercc_count_matrix_new,
file = "./results/matrice_count/ercc_matrices.txt",
quote = F,
@@ -38,7 +44,10 @@ write.table(ercc_count_matrix_new,
ercc_real_concentration <- read_tsv("./data/ercc_concentration.txt") %>%
select(`ERCC ID`, `concentration in Mix 1 (attomoles/ul)`) %>%
- rename(`ERCC ID` = "gene", `concentration in Mix 1 (attomoles/ul)` = "concentration")
+ rename(
+ `ERCC ID` = "gene",
+ `concentration in Mix 1 (attomoles/ul)` = "concentration"
+ )
c_sup0 <- create_correlation_figures(ercc_count_matrix, 0)
c_sup2 <- create_correlation_figures(ercc_count_matrix, 2)
@@ -88,8 +97,9 @@ data_sample <- get_sample_count(data_count_matrix)
ercc_sample <- get_sample_count(ercc_count_matrix)
relative_counts <- get_relative_count(data_sample, ercc_sample)
relative_counts <- relative_counts %>% arrange(name)
-pdf("./results/ERCC_analysis/ratio_ercc_on_genecount.pdf",
- width = 12, height = 8)
+pdf("./results/ERCC_analysis/ratio_ercc_on_genecount.pdf",
+ width = 12, height = 8
+)
ggplot(relative_counts, mapping = aes(x = name, y = relative_count)) +
geom_boxplot() +
theme(axis.text.x = element_text(angle = 90))
@@ -97,7 +107,9 @@ dev.off()
# Normalisation
full_matrix <- rbind(data_count_matrix, ercc_count_matrix)
-coldata <- data.frame(condition = relevel(as.factor(str_extract(colnames(data_count_matrix), "BRAF|DMSO")), "DMSO"))
+coldata <- data.frame(condition = relevel(
+ as.factor(str_extract(colnames(data_count_matrix), "BRAF|DMSO")), "DMSO"
+))
rownames(coldata) <- colnames(data_count_matrix)
dds <- DESeqDataSetFromMatrix(
countData = full_matrix, colData = coldata,
--
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