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plots: Unify colors

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This commit is contained in:
Elias Projahn 2022-03-01 15:49:04 +01:00
parent 2fb48be0e3
commit 2427e8c0c0
1 changed files with 65 additions and 20 deletions
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85
R/plots.R
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@ -1,3 +1,17 @@
#' Base color for the plots.
#' @noRd
base_color <- function() "#1964bf"
#' Transparent version of the base color.
#' @noRd
base_color_transparent <- function() "#1964bf80"
#' Color palette for gene sets.
#' @noRd
gene_set_color <- function(index) {
c("#FF7F00", "#4DAF4A", "#984EA3")[index]
}
#' Plot gene positions.
#'
#' This function requires the package `plotly`.
@ -23,7 +37,7 @@ plot_positions <- function(species_ids, gene_sets) {
# Prefilter species.
species <- geposan::species[id %chin% species_ids]
plot <- plotly::plot_ly(colors = "Set2") |>
plot <- plotly::plot_ly() |>
plotly::layout(
xaxis = list(
title = "Species",
@ -36,7 +50,8 @@ plot_positions <- function(species_ids, gene_sets) {
data = species_max_distance,
x = ~species,
y = ~max_distance,
color = "All genes"
name = "All genes",
marker = list(color = base_color())
)
if (length(gene_sets) > 0) {
@ -48,6 +63,8 @@ plot_positions <- function(species_ids, gene_sets) {
by.y = "id"
)
index <- 1
for (gene_set_name in names(gene_sets)) {
gene_set <- gene_sets[[gene_set_name]]
@ -56,9 +73,14 @@ plot_positions <- function(species_ids, gene_sets) {
x = ~species,
y = ~distance,
text = ~name,
color = gene_set_name,
marker = list(size = 10, opacity = 0.66)
name = gene_set_name,
marker = list(
size = 10,
color = gene_set_color(index)
)
)
index <- index + 1
}
}
@ -85,7 +107,7 @@ plot_rankings <- function(rankings, gene_sets) {
stop("Please install \"plotly\" to use this function.")
}
plot <- plotly::plot_ly(colors = "Set2") |>
plot <- plotly::plot_ly() |>
plotly::layout(
xaxis = list(tickvals = names(rankings)),
yaxis = list(title = "Score")
@ -100,12 +122,14 @@ plot_rankings <- function(rankings, gene_sets) {
data = ranking,
x = ranking_name,
y = ~score,
color = "All genes",
name = "All genes",
type = "violin",
spanmode = "hard",
points = FALSE,
showlegend = is_first,
hoverinfo = "skip"
hoverinfo = "skip",
line = list(color = base_color()),
fillcolor = base_color_transparent()
)
if (length(gene_sets) > 0) {
@ -116,6 +140,8 @@ plot_rankings <- function(rankings, gene_sets) {
by.y = "id"
)
index <- 1
for (gene_set_name in names(gene_sets)) {
gene_set <- gene_sets[[gene_set_name]]
@ -123,7 +149,7 @@ plot_rankings <- function(rankings, gene_sets) {
data = gene_set_data[gene %chin% gene_set],
x = ranking_name,
y = ~score,
color = gene_set_name,
name = gene_set_name,
text = ~name,
customdata = ~percentile,
hovertemplate = paste0(
@ -133,8 +159,13 @@ plot_rankings <- function(rankings, gene_sets) {
"<extra></extra>"
),
showlegend = is_first,
marker = list(size = 20, opacity = 0.66)
marker = list(
size = 10,
color = gene_set_color(index)
)
)
index <- index + 1
}
}
@ -167,14 +198,14 @@ plot_scores <- function(ranking, gene_sets = NULL, max_rank = NULL) {
n_ranks <- nrow(ranking)
sample_ranking <- ranking[seq(1, n_ranks, 5)]
plot <- plotly::plot_ly(colors = "Set2") |>
plot <- plotly::plot_ly() |>
plotly::add_lines(
data = sample_ranking,
x = ~percentile,
y = ~score,
color = "All genes",
name = "All genes",
hoverinfo = "skip",
line = list(width = 4)
line = list(width = 4, color = base_color())
) |>
plotly::layout(
xaxis = list(
@ -193,6 +224,8 @@ plot_scores <- function(ranking, gene_sets = NULL, max_rank = NULL) {
by.y = "id"
)
index <- 1
for (gene_set_name in names(gene_sets)) {
gene_set <- gene_sets[[gene_set_name]]
@ -200,7 +233,7 @@ plot_scores <- function(ranking, gene_sets = NULL, max_rank = NULL) {
data = gene_set_data[gene %chin% gene_set],
x = ~percentile,
y = ~score,
color = gene_set_name,
name = gene_set_name,
text = ~name,
customdata = ~rank,
hovertemplate = paste0(
@ -210,8 +243,13 @@ plot_scores <- function(ranking, gene_sets = NULL, max_rank = NULL) {
"Percentile: %{x:.2%}",
"<extra></extra>"
),
marker = list(size = 20, opacity = 0.66)
marker = list(
size = 10,
color = gene_set_color(index)
)
)
index <- index + 1
}
}
@ -254,13 +292,14 @@ plot_boxplot <- function(ranking, gene_sets = NULL) {
stop("Please install \"plotly\" to use this function.")
}
plot <- plotly::plot_ly(colors = "Set2") |>
plot <- plotly::plot_ly() |>
plotly::add_boxplot(
data = ranking,
x = "All genes",
y = ~score,
color = "All genes",
showlegend = FALSE
name = "All genes",
showlegend = FALSE,
line = list(color = base_color())
) |>
plotly::layout(
xaxis = list(tickvals = c("All genes", names(gene_sets))),
@ -268,6 +307,8 @@ plot_boxplot <- function(ranking, gene_sets = NULL) {
)
if (length(gene_sets) > 0) {
index <- 1
for (gene_set_name in names(gene_sets)) {
gene_set <- gene_sets[[gene_set_name]]
@ -275,9 +316,12 @@ plot_boxplot <- function(ranking, gene_sets = NULL) {
data = ranking[gene %chin% gene_set],
x = gene_set_name,
y = ~score,
color = gene_set_name,
showlegend = FALSE
name = gene_set_name,
showlegend = FALSE,
line = list(color = gene_set_color(index))
)
index <- index + 1
}
}
@ -323,7 +367,8 @@ plot_chromosomes <- function(ranking) {
data = data,
x = ~chromosome,
y = ~score,
type = "bar"
type = "bar",
marker = list(color = base_color())
) |>
plotly::layout(
xaxis = list(