From 111882dc03a556d90fa36b8941c789eeab4db4d1 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Wed, 25 Sep 2024 13:15:24 +0200
Subject: [PATCH] fix figures
---
R/figure.R | 34 ++++++++++++++++++++--------------
1 file changed, 20 insertions(+), 14 deletions(-)
diff --git a/R/figure.R b/R/figure.R
index 07a53b1..1b98bd7 100644
--- a/R/figure.R
+++ b/R/figure.R
@@ -17,10 +17,12 @@ build_figure <- function(top_go_result, go_term_type, outfile) {
}
top_go_result$fish <- as.numeric(gsub("< ", "", top_go_result$fish))
top_go_result <- top_go_result %>%
- mutate(sigv = -log10(padj),
- significance = ifelse(sigv < 400, sigv, 400),
- ft = paste(GO.ID, ":", Term)) %>%
- filter(padj <= 0.05) %>%
+ mutate(
+ sigv = -log10(padj),
+ significance = ifelse(sigv < 400, sigv, 400),
+ ft = paste(GO.ID, ":", Term)
+ ) %>%
+ filter(pvalue <= 0.05) %>%
arrange(desc(significance))
fig <- ggplot(top_go_result, mapping = aes(
x = significance, y = fct_reorder(ft, significance),
@@ -30,19 +32,23 @@ build_figure <- function(top_go_result, go_term_type, outfile) {
if (min(top_go_result$significance) * 0.95 < -log10(0.05)) {
fig <- fig +
geom_vline(aes(xintercept = -log10(0.05), linetype = "significance"),
- size = 0.5, color = "black") +
+ size = 0.5, color = "black"
+ ) +
scale_linetype_manual(
- name = "Vertical line", values=c(2, 2),
- guide = guide_legend(override.aes = list(size = c(0.5))))
+ name = "Vertical line", values = c(2, 2),
+ guide = guide_legend(override.aes = list(size = c(0.5)))
+ )
}
fig <- fig +
- geom_point() +
- xlab("-log10(pvalue)") +
- ylab(go_name) +
- theme_bw() +
- coord_cartesian(xlim = c(min(top_go_result$significance, 50) * 0.95,
- max(top_go_result$significance)) * 1.05) +
- guides(color = "none", size = guide_legend(title = "# input genes"))
+ geom_point() +
+ xlab("-log10(padj)") +
+ ylab(go_name) +
+ theme_bw() +
+ coord_cartesian(xlim = c(
+ min(top_go_result$significance, 50) * 0.95,
+ max(top_go_result$significance)
+ ) * 1.05) +
+ guides(color = "none", size = guide_legend(title = "# input genes"))
if (max(top_go_result$significance) > 100) {
fig <- fig + scale_x_log10()
}
--
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