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Implement gene set highlighting in positions plot

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This commit is contained in:
Elias Projahn 2022-05-18 17:29:35 +02:00
parent 7e53015168
commit e41d02c659
2 changed files with 26 additions and 2 deletions
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23
R/plots.R
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@ -385,12 +385,16 @@ plot_chromosomes <- function(ranking) {
#' #'
#' @param ranking The ranking to visualize. #' @param ranking The ranking to visualize.
#' @param chromosome_name The chromosome to visualize. #' @param chromosome_name The chromosome to visualize.
#' @param gene_sets Named list of vectors of genes to highlight. The list names
#' will be used as labels.
#' #'
#' @return A `plotly` figure. #' @return A `plotly` figure.
#' @seealso ranking() #' @seealso ranking()
#' #'
#' @export #' @export
plot_scores_by_position <- function(ranking, chromosome_name) { plot_scores_by_position <- function(ranking,
chromosome_name,
gene_sets = NULL) {
if (!requireNamespace("plotly", quietly = TRUE)) { if (!requireNamespace("plotly", quietly = TRUE)) {
stop("Please install \"plotly\" to use this function.") stop("Please install \"plotly\" to use this function.")
} }
@ -406,11 +410,28 @@ plot_scores_by_position <- function(ranking, chromosome_name) {
by = "gene" by = "gene"
) )
data[, `:=`(gene_set = "All genes", color = base_color())]
index <- 1
for (gene_set_name in names(gene_sets)) {
gene_set_genes <- gene_sets[[gene_set_name]]
data[
gene %chin% gene_set_genes,
`:=`(
gene_set = gene_set_name,
color = gene_set_color(index)
)
]
index <- index + 1
}
plotly::plot_ly() |> plotly::plot_ly() |>
plotly::add_markers( plotly::add_markers(
data = data, data = data,
x = ~start_position, x = ~start_position,
y = ~score, y = ~score,
name = ~gene_set,
hoverinfo = "skip" hoverinfo = "skip"
) |> ) |>
plotly::layout( plotly::layout(

5
man/plot_scores_by_position.Rd
View file

@ -4,12 +4,15 @@
\alias{plot_scores_by_position} \alias{plot_scores_by_position}
\title{Plot scores in relation to chromosomal position of genes.} \title{Plot scores in relation to chromosomal position of genes.}
\usage{ \usage{
plot_scores_by_position(ranking, chromosome_name) plot_scores_by_position(ranking, chromosome_name, gene_sets = NULL)
} }
\arguments{ \arguments{
\item{ranking}{The ranking to visualize.} \item{ranking}{The ranking to visualize.}
\item{chromosome_name}{The chromosome to visualize.} \item{chromosome_name}{The chromosome to visualize.}
\item{gene_sets}{Named list of vectors of genes to highlight. The list names
will be used as labels.}
} }
\value{ \value{
A \code{plotly} figure. A \code{plotly} figure.