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

Feature dotplot size #54

Merged
merged 3 commits into from
Oct 22, 2023
Merged

Feature dotplot size #54

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
dfcd960
fixed dotplot by genesetsize
tetomonti Oct 20, 2023
66c2d2f
hits list modified to have space-comma-space as separator (it is now …
tetomonti Oct 20, 2023
f9a1b16
Update Version
andrewdchen Oct 20, 2023
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
2 changes: 1 addition & 1 deletion DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: hypeR
Title: An R Package For Geneset Enrichment Workflows
Version: 1.99.0
Version: 1.99.1
Authors@R: c(person(given="Anthony", family="Federico", email="[email protected]",
role=c("aut", "cre")),
person(given="Andrew", family="Chen", email="[email protected]",
Expand Down
34 changes: 24 additions & 10 deletions R/hyp_dots.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@
.dots_multi_plot <- function(multihyp_data,
top=20,
abrv=50,
size_by=c("genesets", "significance", "none"),
size_by=c("genesets", "significance", "overlap", "none"),
pval_cutoff=1,
fdr_cutoff=1,
val=c("fdr", "pval"),
Expand Down Expand Up @@ -79,16 +79,29 @@

if (size_by == "significance") {
df.melted$size <- df.melted$significance
}

if (size_by == "genesets") {
} else if (size_by == "genesets") {
geneset.sizes <- lapply(multihyp_data, function(hyp_obj) {
hyp_obj$data[, c("label", "geneset")]
}) %>%
do.call(rbind, .) %>%
dplyr::distinct(label, .keep_all=TRUE) %>%
dplyr::pull(geneset, label)
df.melted$size <- geneset.sizes[df.melted$label]
#df.melted$size <- geneset.sizes[df.melted$label]
names(geneset.sizes) <- substr(names(geneset.sizes), 1, abrv)
stopifnot( all(!is.na(match_idx <- match(df.melted$label,names(geneset.sizes)))) )
df.melted$size <- geneset.sizes[match_idx]
} else if (size == "overlap") {
stop( "size_by overlap not implemented yet")
overlap.sizes <- lapply(multihyp_data, function(hyp_obj) {
hyp_obj$data[, c("label", "overlap")]
}) %>%
do.call(rbind, .) %>%
dplyr::distinct(label, .keep_all=TRUE) %>%
dplyr::pull(overlap, label)
#df.melted$size <- overlap.sizes[df.melted$label]
names(overlap.sizes) <- substr(names(overlap.sizes), 1, abrv)
stopifnot( all(!is.na(match_idx <- match(df.melted$label,names(overlap.sizes)))) )
df.melted$size <- overlap.sizes[match_idx]
}

p <- df.melted %>%
Expand All @@ -104,14 +117,15 @@

if (size_by == "none") {
p <- p + guides(size="none")
}
if (size_by == "significance") {
} else if (size_by == "significance") {
p <- p + scale_size_continuous(trans=.reverselog_trans(10)) + labs(size="Significance")
}
if (size_by == "genesets") {
} else if (size_by == "genesets" ) {
p <- p + scale_size_continuous(trans=scales::log10_trans()) + labs(size="Genesets\nSize")
} else if (size_by == "overlap" ) {
p <- p + scale_size_continuous(trans=scales::log10_trans()) + labs(size="Overlap\nSize")
} else {
stop("unrecognized 'size_by':", size_by)
}

return(p)
}

Expand Down
3 changes: 2 additions & 1 deletion R/hyper_enrichment.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,8 @@
geneset=n.genesets,
overlap=n.hits,
background=background,
hits=sapply(genesets, function(x, y) paste(intersect(x, y), collapse=','), signature.found),
#hits=sapply(genesets, function(x, y) paste(intersect(x, y), collapse=','), signature.found),
hits=sapply(genesets, function(x, y) paste(intersect(x, y), collapse=' , '), signature.found),
stringsAsFactors=FALSE)

# Handle plots
Expand Down