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Add option to show all chromosomes in positions plot

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This commit is contained in:
Elias Projahn 2022-05-23 11:40:28 +02:00
parent d83dfa0574
commit a1e6147466
3 changed files with 36 additions and 20 deletions
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2
DESCRIPTION
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@ -17,7 +17,7 @@ Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
RoxygenNote: 7.2.0
Depends:
R (>= 2.10)
Imports:

48
R/plots.R
View file

@ -74,7 +74,7 @@ plot_positions <- function(species_ids, gene_sets) {
x = ~species,
y = ~distance,
name = gene_set_name,
text = ~glue::glue(
text = ~ glue::glue(
"<b>{name}</b><br>",
"{round(distance / 1000000, digits = 2)} MBp"
),
@ -155,7 +155,7 @@ plot_rankings <- function(rankings, gene_sets) {
x = ranking_name,
y = ~score,
name = gene_set_name,
text = ~glue::glue(
text = ~ glue::glue(
"<b>{name}</b><br>",
"Score: {round(score, digits = 2)}<br>",
"Rank: {rank}<br>",
@ -238,7 +238,7 @@ plot_scores <- function(ranking, gene_sets = NULL, max_rank = NULL) {
x = ~percentile,
y = ~score,
name = gene_set_name,
text = ~glue::glue(
text = ~ glue::glue(
"<b>{name}</b><br>",
"Score: {round(score, digits = 2)}<br>",
"Rank: {rank}<br>",
@ -385,7 +385,9 @@ plot_chromosomes <- function(ranking) {
#' Plot scores in relation to chromosomal position of genes.
#'
#' @param ranking The ranking to visualize.
#' @param chromosome_name The chromosome to visualize.
#' @param chromosome_name The chromosome to visualize. If this is `NULL` all,
#' chromosomes will be included and the x-axis will show distances instead of
#' positions.
#' @param gene_sets Named list of vectors of genes to highlight. The list names
#' will be used as labels.
#'
@ -394,22 +396,23 @@ plot_chromosomes <- function(ranking) {
#'
#' @export
plot_scores_by_position <- function(ranking,
chromosome_name,
chromosome_name = NULL,
gene_sets = NULL) {
if (!requireNamespace("plotly", quietly = TRUE)) {
stop("Please install \"plotly\" to use this function.")
}
chromosome_name_ <- chromosome_name
data <- merge(
ranking,
distance_data <- if (!is.null(chromosome_name)) {
chromosome_name_ <- chromosome_name
geposan::distances[
species == "hsapiens" &
chromosome_name == chromosome_name_
],
by = "gene"
)
]
} else {
geposan::distances[species == "hsapiens"]
}
data <- merge(ranking, distance_data, by = "gene")
data <- merge(
data,
@ -434,16 +437,23 @@ plot_scores_by_position <- function(ranking,
index <- index + 1
}
# Use distances instead of positions in case all chromosomes are included.
if (is.null(chromosome_name)) {
data[, x := distance]
} else {
data[, x := start_position]
}
plotly::plot_ly() |>
plotly::add_markers(
data = data,
x = ~start_position,
x = ~x,
y = ~score,
name = ~gene_set,
text = ~glue::glue(
text = ~ glue::glue(
"<b>{name}</b><br>",
"Position: ",
"{round(start_position / 1000000, digits = 2)} MBp<br>",
if (is.null(chromosome_name)) "Distance: " else "Position: ",
"{round(x / 1000000, digits = 2)} MBp<br>",
"Score: {round(score, digits = 2)}<br>",
"Rank: {rank}<br>",
"Percentile: {round(percentile * 100, digits = 2)}%"
@ -451,7 +461,11 @@ plot_scores_by_position <- function(ranking,
hoverinfo = "text",
) |>
plotly::layout(
xaxis = list(title = "Position (Bp)"),
xaxis = list(title = if (is.null(chromosome_name)) {
"Distance (Bp)"
} else {
"Position (Bp)"
}),
yaxis = list(title = "Score")
)
}

6
man/plot_scores_by_position.Rd
View file

@ -4,12 +4,14 @@
\alias{plot_scores_by_position}
\title{Plot scores in relation to chromosomal position of genes.}
\usage{
plot_scores_by_position(ranking, chromosome_name, gene_sets = NULL)
plot_scores_by_position(ranking, chromosome_name = NULL, gene_sets = NULL)
}
\arguments{
\item{ranking}{The ranking to visualize.}
\item{chromosome_name}{The chromosome to visualize.}
\item{chromosome_name}{The chromosome to visualize. If this is \code{NULL} all,
chromosomes will be included and the x-axis will show distances instead of
positions.}
\item{gene_sets}{Named list of vectors of genes to highlight. The list names
will be used as labels.}