Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

issue-24 fixing bug for volcano labels #25

Merged
merged 2 commits into from
Mar 15, 2024
Merged

issue-24 fixing bug for volcano labels #25

Changes from 1 commit
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
17719f3
issue-24 fixing bug for volcano labels
delfarahalireza Mar 15, 2024
71db1e6
Merge branch 'main' into issue-24
delfarahalireza Mar 15, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
41 changes: 23 additions & 18 deletions R/differential_expression.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -292,11 +292,10 @@ diffex_fdr <- function(term_data) {
#'
#' @export
plot_volcano <- function(
regression_significance,
max_p_trans = 10,
FDR_cutoff = 0.1,
feature_labels = NULL
) {
regression_significance,
max_p_trans = 10,
FDR_cutoff = 0.1,
feature_labels = NULL) {

checkmate::assertDataFrame(regression_significance)
stopifnot("term" %in% colnames(regression_significance))
Expand All @@ -311,24 +310,30 @@ plot_volcano <- function(
stop("volcano plot cannot be generated due to unknown test")
}

regression_significance %>%
dplyr::filter(!is.na(p.value)) %>%
dplyr::mutate(
p.value.trans = trans_pvalues(p.value, max_p_trans = max_p_trans),
is_discovery = qvalue < FDR_cutoff
) %>%
ggplot(aes_string(x = effect_var)) +
{if ("compoundName" %in% colnames(regression_significance)) {
geom_point(aes(y = p.value.trans, color = is_discovery, name = compoundName)) +
geom_text(aes(label = ifelse(compoundName %in% feature_labels, compoundName, ""), y = p.value.trans, vjust = -0.75))
}
else {geom_point(aes(y = p.value.trans, color = is_discovery))}
} +
grob <- ggplot(
regression_significance %>%
dplyr::filter(!is.na(p.value)) %>%
dplyr::mutate(
p.value.trans = trans_pvalues(p.value, max_p_trans = max_p_trans),
is_discovery = qvalue < FDR_cutoff
),
aes_string(x = effect_var)
) +
facet_wrap(~term, scales = "free_x") +
scale_x_continuous("Effect size") +
scale_y_continuous(expression(-log[10] ~ "pvalue")) +
scale_color_manual(values = c("FALSE" = "gray50", "TRUE" = "RED")) +
theme_bw()

if ("compoundName" %in% colnames(regression_significance)) {
grob <- grob +
geom_point(aes(y = p.value.trans, color = is_discovery, name = compoundName)) +
geom_text(aes(label = ifelse(compoundName %in% feature_labels, compoundName, ""), y = p.value.trans, vjust = -0.75))
} else {
grob <- grob +
geom_point(aes(y = p.value.trans, color = is_discovery))
}
return(grob)
}

trans_pvalues <- function(p, max_p_trans = 10) {
Expand Down