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

Jump to bottom

Added parameter to adjust the size of gene tags #72

Merged
merged 3 commits into from
Jul 24, 2024
Merged

Added parameter to adjust the size of gene tags #72

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
873bf89
Update do_VolcanoPlot.R
nbpeterson3 Jul 19, 2024
e544473
Update do_VolcanoPlot.R
nbpeterson3 Jul 19, 2024
5e2804c
Update do_VolcanoPlot.R
nbpeterson3 Jul 19, 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
11 changes: 8 additions & 3 deletions R/do_VolcanoPlot.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
#' @param add_gene_tags \strong{\code{\link[base]{logical}}} | Whether to plot the top genes.
#' @param add_tag_side \strong{\code{\link[base]{logical}}} | Either "both", "positive" or "negative" to indicate which side of genes to tag
#' @param order_tags_by \strong{\code{\link[base]{character}}} | Either "both", "pvalue" or "logfc".
#' @param tag_size \strong{\code{\link[base]{numeric}}} | Size of the text/label for the tags.
#' @param n_genes \strong{\code{\link[base]{numeric}}} | Number of top genes to plot.
#' @param use_labels \strong{\code{\link[base]{logical}}} | Whether to use labels instead of text for the tags.
#' @param colors.use \strong{\code{\link[base]{character}}} | Color to generate a tetradic color scale with.
Expand All @@ -36,6 +37,7 @@ do_VolcanoPlot <- function(sample,
add_gene_tags = TRUE,
add_tag_side = "both",
order_tags_by = "both",
tag_size = 6,
n_genes = 5,
use_labels = FALSE,
colors.use = "steelblue",
Expand Down Expand Up @@ -65,7 +67,8 @@ do_VolcanoPlot <- function(sample,
"border.size" = border.size,
"font.size" = font.size,
"line_size" = line_size,
"n_genes" = n_genes)
"n_genes" = n_genes,
"tag_size" = tag_size)
check_type(parameters = numeric_list, required_type = "numeric", test_function = is.numeric)
# Check character parameters.
character_list <- list("border.color" = border.color,
Expand Down Expand Up @@ -222,14 +225,16 @@ do_VolcanoPlot <- function(sample,
mapping = ggplot2::aes(label = .data$gene),
max.overlaps = 1000,
color = "black",
fontface = "bold")
fontface = "bold",
size = tag_size)
} else if (isTRUE(use_labels)){
p <- p +
ggrepel::geom_label_repel(data = data.label,
mapping = ggplot2::aes(label = .data$gene),
max.overlaps = 1000,
color = "black",
fontface = "bold")
fontface = "bold",
size = tag_size)
}

}
Expand Down
Loading