-
Notifications
You must be signed in to change notification settings - Fork 2
Open
Description
Hi January!
I have been using your package for a quite long time and I found a bug in the new (ggplot) implementation of the evidence plot. Here's the reprex:
library(tmod)
library(tibble)
genesets <- tribble(
~gene_symbol, ~geneset,
"gene1", "diseaseA",
"gene2", "diseaseA",
"gene3", "diseaseA",
"gene4", "diseaseB",
"gene5", "diseaseB",
"gene6", "diseaseB",
"gene7", "diseaseC",
"gene8", "diseaseC",
"gene9", "diseaseC",
"gene10", "diseaseC"
)
tmod_db <- tmod::makeTmodFromDataFrame(
genesets,
feature_col = "gene_symbol",
module_col = "geneset",
title_col = "geneset"
)
ranked_genes <- paste0("gene", 1:10)res <- tmod::tmodCERNOtest(ranked_genes, mset = tmod_db, qval = 1)
# Function with bug
tmod::ggEvidencePlot(
ranked_genes,
m = c("diseaseA", "diseaseB"),
mset = tmod_db,
gene.labels = FALSE
)
# Old implementation is correct
tmod::evidencePlot(
ranked_genes,
m = c("diseaseA", "diseaseB"),
mset = tmod_db,
gene.labels = FALSE
) Plots:
ggplot version:
original version:
The curves are incorrect in the ggplot version. Is it easy to fix?
Also, there's a warning from the ggplot:
Warning message:
In geom_segment(aes(x = 0, y = 0, xend = length(l_orig), yend = 1), :
All aesthetics have length 1, but the data has 16 rows.
ℹ Please consider using `annotate()` or provide this layer with data containing a single row.
Best wishes,
Paweł
Metadata
Metadata
Assignees
Labels
No labels