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plots: Sort species in input data plot

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This commit is contained in:
Elias Projahn 2022-05-28 17:01:31 +02:00
parent d144f490a0
commit abf78f27d3
2 changed files with 30 additions and 2 deletions
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27
R/plots.R
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@ -19,9 +19,11 @@ gene_set_color <- function(index) {
#' @param species_ids IDs of species to show in the plot.
#' @param gene_sets A list of gene sets (containing vectors of gene IDs) that
#' will be highlighted in the plot. The names will be used as labels.
#' @param reference_gene_ids Optionally, a set of reference genes that will be
#' used to reorder the species.
#'
#' @export
plot_positions <- function(species_ids, gene_sets) {
plot_positions <- function(species_ids, gene_sets, reference_gene_ids = NULL) {
if (!requireNamespace("plotly", quietly = TRUE)) {
stop("Please install \"plotly\" to use this function.")
}
@ -37,11 +39,34 @@ plot_positions <- function(species_ids, gene_sets) {
# Prefilter species.
species <- geposan::species[id %chin% species_ids]
# Sort species if reference genes have been provided.
if (!is.null(reference_gene_ids)) {
species_median_distance <- data[
gene %chin% reference_gene_ids,
.(median_distance = as.numeric(stats::median(distance))),
by = species
]
species <- merge(
species,
species_median_distance,
by.x = "id",
by.y = "species",
all.x = TRUE
)
setorder(species, median_distance)
}
plot <- plotly::plot_ly() |>
plotly::layout(
xaxis = list(title = "Distance to telomeres [Bp]"),
yaxis = list(
title = "Species",
type = "category",
categoryorder = "array",
categoryarray = species$id,
tickmode = "array",
tickvals = species$id,
ticktext = species$name
),

5
man/plot_positions.Rd
View file

@ -4,13 +4,16 @@
\alias{plot_positions}
\title{Plot gene positions.}
\usage{
plot_positions(species_ids, gene_sets)
plot_positions(species_ids, gene_sets, reference_gene_ids = NULL)
}
\arguments{
\item{species_ids}{IDs of species to show in the plot.}
\item{gene_sets}{A list of gene sets (containing vectors of gene IDs) that
will be highlighted in the plot. The names will be used as labels.}
\item{reference_gene_ids}{Optionally, a set of reference genes that will be
used to reorder the species.}
}
\description{
This function requires the package \code{plotly}.