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plots: Refactor and improve
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5 changed files with 125 additions and 138 deletions
231
R/plots.R
231
R/plots.R
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@ -4,62 +4,63 @@
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#'
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#' @param species_ids IDs of species to show in the plot.
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#' @param gene_sets A list of gene sets (containing vectors of gene IDs) that
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#' will be highlighted in the plot.
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#' @param labels Labels for the gene sets. This is required if gene sets are
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#' given and has to have the same length.
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#' @param use_positions Whether to display positions instead of distances.
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#' will be highlighted in the plot. The names will be used as labels.
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#'
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#' @export
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plot_positions <- function(species_ids,
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gene_sets,
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labels,
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use_positions = FALSE) {
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plot_positions <- function(species_ids, gene_sets) {
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if (!requireNamespace("plotly", quietly = TRUE)) {
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stop("Please install \"plotly\" to use this function.")
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}
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data <- merge(
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geposan::distances[gene %chin% unlist(gene_sets) &
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species %chin% species_ids],
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geposan::genes[, .(id, name)],
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by.x = "gene", by.y = "id"
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)
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# Prefilter data by species.
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data <- geposan::distances[species %chin% species_ids]
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if (use_positions) {
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data[, value := position]
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} else {
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data[, value := distance]
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}
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# Add labels for each gene set.
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for (i in seq_along(gene_sets)) {
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data[gene %chin% gene_sets[[i]], label := labels[i]]
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}
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sample_data <- data[sample(nrow(data), 1000)]
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# Prefilter species.
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species <- geposan::species[id %chin% species_ids]
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yaxis_title <- if (use_positions) {
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"Position [Bp]"
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} else {
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"Distance to telomeres [Bp]"
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plot <- plotly::plot_ly(colors = "Set2") |>
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plotly::add_markers(
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data = sample_data,
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x = ~species,
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y = ~distance,
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color = "All genes",
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hoverinfo = "skip"
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) |>
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plotly::layout(
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xaxis = list(
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title = "Species",
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tickvals = species$id,
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ticktext = species$name
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),
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yaxis = list(title = "Distance to telomeres [Bp]")
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)
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if (length(gene_sets) > 0) {
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# Include gene information which will be used for labeling
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gene_set_data <- merge(
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data[gene %chin% unlist(gene_sets)],
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geposan::genes,
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by.x = "gene",
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by.y = "id"
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)
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for (gene_set_name in names(gene_sets)) {
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gene_set <- gene_sets[[gene_set_name]]
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plot <- plot |> plotly::add_markers(
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data = gene_set_data[gene %chin% gene_set],
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x = ~species,
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y = ~distance,
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text = ~name,
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color = gene_set_name,
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marker = list(size = 10, opacity = 0.66)
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)
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}
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}
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plotly::plot_ly(
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data = data,
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x = ~species,
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y = ~value,
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color = ~label,
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text = ~name,
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type = "scatter",
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mode = "markers"
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) |> plotly::layout(
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xaxis = list(
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title = "Species",
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tickvals = species$id,
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ticktext = species$name
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),
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yaxis = list(title = yaxis_title)
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)
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plot
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}
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@ -84,10 +85,7 @@ plot_rankings <- function(rankings, gene_sets) {
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plot <- plotly::plot_ly(colors = "Set2") |>
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plotly::layout(
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xaxis = list(
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title = "Ranking",
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tickvals = names(rankings)
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),
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xaxis = list(tickvals = names(rankings)),
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yaxis = list(title = "Score")
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)
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@ -96,13 +94,6 @@ plot_rankings <- function(rankings, gene_sets) {
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for (ranking_name in names(rankings)) {
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ranking <- rankings[[ranking_name]]
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data <- merge(
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ranking,
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geposan::genes,
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by.x = "gene",
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by.y = "id"
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)
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plot <- plot |> plotly::add_trace(
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data = ranking,
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x = ranking_name,
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@ -115,18 +106,27 @@ plot_rankings <- function(rankings, gene_sets) {
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hoverinfo = "skip"
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)
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for (gene_set_name in names(gene_sets)) {
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gene_set <- gene_sets[[gene_set_name]]
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plot <- plot |> plotly::add_markers(
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data = data[gene %chin% gene_set],
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x = ranking_name,
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y = ~score,
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text = ~name,
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color = gene_set_name,
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showlegend = is_first,
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marker = list(size = 20, opacity = 0.66)
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if (length(gene_sets) > 0) {
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gene_set_data <- merge(
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ranking[gene %chin% unlist(gene_sets)],
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geposan::genes,
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by.x = "gene",
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by.y = "id"
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)
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for (gene_set_name in names(gene_sets)) {
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gene_set <- gene_sets[[gene_set_name]]
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plot <- plot |> plotly::add_markers(
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data = gene_set_data[gene %chin% gene_set],
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x = ranking_name,
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y = ~score,
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text = ~name,
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color = gene_set_name,
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showlegend = is_first,
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marker = list(size = 20, opacity = 0.66)
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)
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}
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}
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is_first <- FALSE
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@ -141,32 +141,25 @@ plot_rankings <- function(rankings, gene_sets) {
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#' This function requires the package `plotly`.
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#'
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#' @param ranking The ranking to visualize.
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#' @param gene_sets A list of gene sets (containing vectors of gene IDs) that
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#' will be highlighted in the plot.
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#' @param labels Labels for the gene sets. This is required if gene sets are
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#' given and has to have the same length.
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#' @param max_rank The maximum rank of the highlighted genes. All genes that
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#' are ranked lower will appear greyed out.
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#' @param gene_sets A named list of gene sets (containing vectors of gene IDs)
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#' that will be highlighted in the plot. The names will be used in the legend.
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#' @param max_rank The maximum rank of included genes. All genes that are ranked
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#' lower will appear greyed out.
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#'
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#' @seealso ranking()
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#'
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#' @export
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plot_scores <- function(ranking,
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gene_sets = NULL,
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labels = NULL,
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max_rank = NULL) {
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plot_scores <- function(ranking, gene_sets = NULL, max_rank = NULL) {
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if (!requireNamespace("plotly", quietly = TRUE)) {
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stop("Please install \"plotly\" to use this function.")
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}
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plot <- plotly::plot_ly() |>
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plotly::add_trace(
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plot <- plotly::plot_ly(colors = "Set2") |>
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plotly::add_markers(
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data = ranking,
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x = ~rank,
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y = ~score,
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color = "All genes",
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type = "scatter",
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mode = "markers",
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hoverinfo = "skip"
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) |>
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plotly::layout(
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@ -175,32 +168,26 @@ plot_scores <- function(ranking,
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)
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if (length(gene_sets) > 0) {
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# Take out the genes to be highlighted.
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gene_set_data <- ranking[gene %chin% unlist(gene_sets)]
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# Add labels for each gene set.
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for (i in seq_along(gene_sets)) {
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gene_set_data[gene %chin% gene_sets[[i]], label := labels[i]]
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}
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# Include gene information which will be used for labeling
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gene_set_data <- merge(
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gene_set_data,
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ranking[gene %chin% unlist(gene_sets)],
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geposan::genes,
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by.x = "gene",
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by.y = "id"
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)
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plot <- plot |> plotly::add_trace(
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data = gene_set_data,
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x = ~rank,
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y = ~score,
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color = ~label,
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text = ~name,
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type = "scatter",
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mode = "markers",
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marker = list(size = 20)
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)
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for (gene_set_name in names(gene_sets)) {
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gene_set <- gene_sets[[gene_set_name]]
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plot <- plot |> plotly::add_markers(
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data = gene_set_data[gene %chin% gene_set],
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x = ~rank,
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y = ~score,
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text = ~name,
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color = gene_set_name,
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marker = list(size = 20, opacity = 0.66)
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)
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}
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}
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@ -231,35 +218,45 @@ plot_scores <- function(ranking,
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#' This function requires the package `plotly`.
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#'
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#' @param ranking The ranking to visualize.
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#' @param gene_sets A list of gene sets (containing vectors of gene IDs) that
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#' will be shown as separate boxes.
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#' @param labels Labels for the gene sets. This is required if gene sets are
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#' given and has to have the same length.
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#' @param gene_sets A named list of gene sets (containing vectors of gene IDs)
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#' that will be shown as separate boxes. The names will be used as labels.
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#'
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#' @seealso ranking()
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#'
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#' @export
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plot_boxplot <- function(ranking, gene_sets = NULL, labels = NULL) {
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plot_boxplot <- function(ranking, gene_sets = NULL) {
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if (!requireNamespace("plotly", quietly = TRUE)) {
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stop("Please install \"plotly\" to use this function.")
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}
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data <- copy(ranking)
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plot <- plotly::plot_ly(colors = "Set2") |>
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plotly::add_boxplot(
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data = ranking,
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x = "All genes",
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y = ~score,
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color = "All genes",
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showlegend = FALSE
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) |>
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plotly::layout(
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xaxis = list(tickvals = c("All genes", names(gene_sets))),
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yaxis = list(title = "Score")
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)
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# Add labels for each gene set.
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for (i in seq_along(gene_sets)) {
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data[gene %chin% gene_sets[[i]], label := labels[i]]
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if (length(gene_sets) > 0) {
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for (gene_set_name in names(gene_sets)) {
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gene_set <- gene_sets[[gene_set_name]]
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plot <- plot |> plotly::add_boxplot(
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data = ranking[gene %chin% gene_set],
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x = gene_set_name,
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y = ~score,
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color = gene_set_name,
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showlegend = FALSE
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)
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}
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}
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# Label the other genes.
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data[!gene %chin% unlist(gene_sets), label := "Other genes"]
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plotly::plot_ly(
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data = data,
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y = ~score,
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color = ~label,
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type = "box"
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)
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plot
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}
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#' Show the distribution of scores across chromosomes.
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