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Add gene selector for custom genes

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This commit is contained in:
Elias Projahn 2022-05-30 21:27:18 +02:00
parent 780e608ee1
commit 5f5670171d
8 changed files with 168 additions and 36 deletions
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56
R/plots.R
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@ -1,35 +1,59 @@
#' Create a plot showing an overview over the provided ranking.
#'
#' @param ranked_data The ranking to visualize.
#' @param highlighted_genes Genes that will be marked.
#' @param sample_proportion Proportion of rows to use as the shown sample.
#'
#' @return A `plotly` figure.
#' @noRd
overview_plot <- function(ranked_data, sample_proportion = 0.05) {
plotly::plot_ly() |>
overview_plot <- function(ranked_data,
highlighted_genes = NULL,
sample_proportion = 0.05) {
figure <- plotly::plot_ly() |>
plotly::add_lines(
data = ranked_data[sample(
nrow(ranked_data),
sample_proportion * nrow(ranked_data)
)],
x = ~rank,
y = ~score
y = ~score,
hoverinfo = "skip"
) |>
plotly::layout(
xaxis = list(title = "Ranks"),
yaxis = list(title = "Score")
)
if (!is.null(highlighted_genes)) {
figure <- figure |>
plotly::add_markers(
data = ranked_data[gene %chin% highlighted_genes],
x = ~rank,
y = ~score,
text = ~ glue::glue(
"<b>{hgnc_name}</b><br>",
"Score: {round(score, digits = 2)}<br>",
"Rank: {rank}<br>",
"Percentile: {round(percentile * 100, digits = 2)}%"
),
hoverinfo = "text",
showlegend = FALSE
)
}
figure
}
#' Create plot showing the distribution of scores using `plotly`.
#'
#' @param ranked_data Data on genes with precomputed ranks.
#' @param highlighted_genes Genes that will be marked.
#' @param ranks How may ranks the x-axis should include. If this parameter is
#' `NULL`, all ranks will be shown.
#'
#' @return A `plotly` figure for rendering.
#' @noRd
scores_plot <- function(ranked_data, ranks = 1000) {
scores_plot <- function(ranked_data, highlighted_genes = NULL, ranks = 1000) {
data <- if (is.null(ranks)) {
ranked_data
} else {
@ -42,20 +66,26 @@ scores_plot <- function(ranked_data, ranks = 1000) {
glue::glue("Ranks (1 to {ranks})")
}
data[, group := data.table::fifelse(
gene %chin% highlighted_genes,
"Your genes",
"All genes"
)]
plotly::plot_ly() |>
plotly::add_markers(
data = data,
x = ~rank,
y = ~score,
text = ~hgnc_name,
customdata = ~percentile,
hovertemplate = paste0(
"<b>%{text}</b><br>",
"Rank: %{x}<br>",
"Score: %{y:.2}<br>",
"Percentile: %{customdata:.2%}",
"<extra></extra>"
)
name = ~group,
text = ~ glue::glue(
"<b>{hgnc_name}</b><br>",
"Score: {round(score, digits = 2)}<br>",
"Rank: {rank}<br>",
"Percentile: {round(percentile * 100, digits = 2)}%"
),
hoverinfo = "text",
showlegend = FALSE
) |>
plotly::layout(
xaxis = list(title = ranks_label),