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plots: Replace max rank with percentile lines

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This commit is contained in:
Elias Projahn 2022-07-22 09:22:16 +02:00
parent 8812c9579f
commit 463faf0fbe
2 changed files with 53 additions and 28 deletions
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76
R/plots.R
View file

@ -212,13 +212,11 @@ plot_rankings <- function(rankings, gene_sets) {
#' @param ranking The ranking to visualize.
#' @param gene_sets A named list of gene sets (containing vectors of gene IDs)
#' that will be highlighted in the plot. The names will be used in the legend.
#' @param max_rank The maximum rank of included genes. All genes that are ranked
#' lower will appear greyed out.
#'
#' @seealso ranking()
#'
#' @export
plot_scores <- function(ranking, gene_sets = NULL, max_rank = NULL) {
plot_scores <- function(ranking, gene_sets = NULL) {
if (!requireNamespace("plotly", quietly = TRUE)) {
stop("Please install \"plotly\" to use this function.")
}
@ -241,7 +239,21 @@ plot_scores <- function(ranking, gene_sets = NULL, max_rank = NULL) {
title = "Percentile",
tickformat = ".0%"
),
yaxis = list(title = "Score")
yaxis = list(title = "Score"),
shapes = list(
vline(0.95),
vline(0.75),
vline(0.50),
vline(0.25),
vline(0.05)
),
annotations = list(
vlineannotation(0.95),
vlineannotation(0.75),
vlineannotation(0.50),
vlineannotation(0.25),
vlineannotation(0.05)
)
)
if (length(gene_sets) > 0) {
@ -280,26 +292,6 @@ plot_scores <- function(ranking, gene_sets = NULL, max_rank = NULL) {
}
}
if (!is.null(max_rank)) {
first_not_included_rank <- max_rank + 1
last_rank <- ranking[, .N]
if (first_not_included_rank <= last_rank) {
plot <- plot |> plotly::layout(
shapes = list(
type = "rect",
fillcolor = "black",
opacity = 0.1,
x0 = 1 - first_not_included_rank / n_ranks,
x1 = 1 - last_rank / n_ranks,
y0 = 0.0,
y1 = 1.0
)
)
}
}
plot
}
@ -494,3 +486,39 @@ plot_scores_by_position <- function(ranking,
yaxis = list(title = "Score")
)
}
#' Helper function for creating a vertical line for plotly.
#' @noRd
vline <- function(x) {
list(
type = "line",
y0 = 0,
y1 = 1,
yref = "paper",
x0 = x,
x1 = x,
line = list(
color = "#00000080",
opacity = 0.5,
dash = "dot"
)
)
}
#' Helper function for creating annotations for lines created using [vline()].
#' @noRd
vlineannotation <- function(x) {
list(
text = glue::glue("{round(x * 100)}%"),
showarrow = FALSE,
yref = "paper",
x = x,
y = 1,
xanchor = "left",
xshift = 4,
align = "left",
font = list(
color = "#00000080"
)
)
}

5
man/plot_scores.Rd
View file

@ -4,16 +4,13 @@
\alias{plot_scores}
\title{Plot a ranking as a scatter plot of scores.}
\usage{
plot_scores(ranking, gene_sets = NULL, max_rank = NULL)
plot_scores(ranking, gene_sets = NULL)
}
\arguments{
\item{ranking}{The ranking to visualize.}
\item{gene_sets}{A named list of gene sets (containing vectors of gene IDs)
that will be highlighted in the plot. The names will be used in the legend.}
\item{max_rank}{The maximum rank of included genes. All genes that are ranked
lower will appear greyed out.}
}
\description{
This function requires the package \code{plotly}.