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plots: Improve hoverinfo in correlation plot

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This commit is contained in:
Elias Projahn 2022-08-17 16:17:22 +02:00
parent 0440d5931c
commit c8b94fade8
2 changed files with 71 additions and 35 deletions
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101
R/plots.R
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@ -215,6 +215,7 @@ plot_rankings <- function(rankings, gene_sets) {
#' @param gene_sets A named list of vectors of gene IDs to highlight. The names
#' will be used to distinguish the sets and in the legend.
#' @param use_ranks Show ranks instead of scores.
#' @param use_sample Limit genes outside of the gene sets to a random sample.
#'
#' @export
plot_rankings_correlation <- function(ranking_x,
@ -222,7 +223,8 @@ plot_rankings_correlation <- function(ranking_x,
name_x,
name_y,
gene_sets = NULL,
use_ranks = TRUE) {
use_ranks = TRUE,
use_sample = TRUE) {
if (!requireNamespace("plotly", quietly = TRUE)) {
stop("Please install \"plotly\" to use this function.")
}
@ -241,12 +243,11 @@ plot_rankings_correlation <- function(ranking_x,
stats::predict(model, model_data, interval = "confidence")
)]
# Take a random sample to actually plot.
sample_data <- data[!gene %chin% unlist(gene_sets)][sample(.N, 1000)]
fig <- plotly::plot_ly()
fig <- plotly::plot_ly() |>
plotly::add_markers(
data = sample_data,
if (use_sample) {
fig <- fig |> plotly::add_markers(
data = data[!gene %chin% unlist(gene_sets)][sample(.N, 1000)],
x = ~x,
y = ~y,
name = "All genes",
@ -255,7 +256,30 @@ plot_rankings_correlation <- function(ranking_x,
size = 5
),
hoverinfo = "skip"
) |>
)
} else {
fig <- fig |> plotly::add_markers(
data = data,
x = ~x,
y = ~y,
name = "All genes",
marker = list(
color = base_color(),
size = 5
),
text = ~ glue::glue(
"<b>{name}</b>",
"<br>",
"{name_x}: {round(x, digits = 2)} ",
"({round(percentile.x * 100, digits = 2)}%)<br>",
"{name_y}: {round(y, digits = 2)} ",
"({round(percentile.y * 100, digits = 2)}%)"
),
hoverinfo = "text"
)
}
fig <- fig |>
plotly::add_lines(
data = model_data,
x = ~x,
@ -276,6 +300,7 @@ plot_rankings_correlation <- function(ranking_x,
)
gene_set_index <- 1
for (gene_set_name in names(gene_sets)) {
gene_set <- gene_sets[[gene_set_name]]
@ -285,11 +310,19 @@ plot_rankings_correlation <- function(ranking_x,
x = ~x,
y = ~y,
name = gene_set_name,
text = ~name,
marker = list(
color = gene_set_color(gene_set_index),
size = 8
)
),
text = ~ glue::glue(
"<b>{name}</b>",
"<br>",
"{name_x}: {round(x, digits = 2)} ",
"({round(percentile.x * 100, digits = 2)}%)<br>",
"{name_y}: {round(y, digits = 2)} ",
"({round(percentile.y * 100, digits = 2)}%)"
),
hoverinfo = "text"
)
gene_set_index <- gene_set_index + 1
@ -565,7 +598,7 @@ plot_scores_by_position <- function(ranking,
"Rank: {rank}<br>",
"Percentile: {round(percentile * 100, digits = 2)}%"
),
marker = list(
marker = list(
color = base_color(),
size = 5
),
@ -580,33 +613,33 @@ plot_scores_by_position <- function(ranking,
yaxis = list(title = "Score")
)
index <- 1
index <- 1
for (gene_set_name in names(gene_sets)) {
gene_set_genes <- gene_sets[[gene_set_name]]
for (gene_set_name in names(gene_sets)) {
gene_set_genes <- gene_sets[[gene_set_name]]
fig <- fig |>
plotly::add_markers(
data = data[gene %chin% gene_set_genes],
x = ~x,
y = ~score,
name = gene_set_name,
text = ~ glue::glue(
"<b>{name}</b><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)}%"
),
marker = list(
color = gene_set_color(index),
size = 8
),
hoverinfo = "text"
)
fig <- fig |>
plotly::add_markers(
data = data[gene %chin% gene_set_genes],
x = ~x,
y = ~score,
name = gene_set_name,
text = ~ glue::glue(
"<b>{name}</b><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)}%"
),
marker = list(
color = gene_set_color(index),
size = 8
),
hoverinfo = "text"
)
index <- index + 1
index <- index + 1
}
fig

5
man/plot_rankings_correlation.Rd
View file

@ -10,7 +10,8 @@ plot_rankings_correlation(
name_x,
name_y,
gene_sets = NULL,
use_ranks = TRUE
use_ranks = TRUE,
use_sample = TRUE
)
}
\arguments{
@ -26,6 +27,8 @@ plot_rankings_correlation(
will be used to distinguish the sets and in the legend.}
\item{use_ranks}{Show ranks instead of scores.}
\item{use_sample}{Limit genes outside of the gene sets to a random sample.}
}
\description{
This function requires the package \code{plotly}.