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123 lines
3.1 KiB
R
123 lines
3.1 KiB
R
#' Create a plot showing an overview over the provided ranking.
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#'
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#' @param ranked_data The ranking to visualize.
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#' @param highlighted_genes Genes that will be marked.
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#' @param sample_proportion Proportion of rows to use as the shown sample.
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#'
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#' @return A `plotly` figure.
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#' @noRd
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overview_plot <- function(ranked_data,
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highlighted_genes = NULL,
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sample_proportion = 0.05) {
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figure <- plotly::plot_ly() |>
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plotly::add_lines(
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data = ranked_data[sample(
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nrow(ranked_data),
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sample_proportion * nrow(ranked_data)
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)],
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x = ~rank,
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y = ~score,
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hoverinfo = "skip"
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) |>
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plotly::layout(
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xaxis = list(title = "Ranks"),
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yaxis = list(title = "Score")
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)
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if (length(highlighted_genes) > 0) {
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figure <- figure |>
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plotly::add_markers(
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data = ranked_data[gene %chin% highlighted_genes],
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x = ~rank,
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y = ~score,
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text = ~ glue::glue(
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"<b>{hgnc_name}</b><br>",
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"Score: {round(score, digits = 2)}<br>",
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"Rank: {rank}<br>",
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"Percentile: {round(percentile * 100, digits = 2)}%"
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),
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hoverinfo = "text",
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showlegend = FALSE
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)
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}
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figure
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}
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#' Create a plot comparing some genes with the overall ranking.
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#'
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#' @param ranked_data The ranking to visualize.
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#' @param highlighted_genes Genes that will be compared.
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#'
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#' @return A `plotly` figure.
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#' @noRd
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box_plot <- function(ranked_data, highlighted_genes) {
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data <- data.table::copy(ranked_data)
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data[, group := data.table::fifelse(
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gene %chin% highlighted_genes,
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"Your genes",
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"Other genes"
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)]
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plotly::plot_ly() |>
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plotly::add_boxplot(
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data = data,
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x = ~score,
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y = ~group,
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boxpoints = FALSE
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) |> plotly::layout(
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xaxis = list(title = "Score"),
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yaxis = list(title = "")
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)
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}
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#' Create plot showing the distribution of scores using `plotly`.
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#'
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#' @param ranked_data Data on genes with precomputed ranks.
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#' @param highlighted_genes Genes that will be marked.
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#' @param ranks How may ranks the x-axis should include. If this parameter is
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#' `NULL`, all ranks will be shown.
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#'
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#' @return A `plotly` figure for rendering.
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#' @noRd
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scores_plot <- function(ranked_data, highlighted_genes = NULL, ranks = 1000) {
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data <- if (is.null(ranks)) {
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ranked_data
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} else {
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ranked_data[1:ranks]
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}
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ranks_label <- if (is.null(ranks)) {
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"Ranks"
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} else {
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glue::glue("Ranks (1 to {ranks})")
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}
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data[, group := data.table::fifelse(
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gene %chin% highlighted_genes,
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"Your genes",
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"All genes"
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)]
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plotly::plot_ly() |>
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plotly::add_markers(
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data = data,
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x = ~rank,
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y = ~score,
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name = ~group,
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text = ~ glue::glue(
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"<b>{hgnc_name}</b><br>",
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"Score: {round(score, digits = 2)}<br>",
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"Rank: {rank}<br>",
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"Percentile: {round(percentile * 100, digits = 2)}%"
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),
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hoverinfo = "text",
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showlegend = FALSE
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) |>
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plotly::layout(
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xaxis = list(title = ranks_label),
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yaxis = list(title = "Score"),
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clickmode = "event+select",
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dragmode = "select"
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)
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}
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