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Retrieve input data using biomaRt

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This commit is contained in:
Elias Projahn 2021-09-16 00:06:54 +02:00
parent 040aabc610
commit 1cea6c3631
205 changed files with 187 additions and 3296961 deletions
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15
scatter_plot.R
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@ -3,23 +3,24 @@ library(ggplot2)
#' Draw a scatter plot containing gene positions.
#'
#' @param input Input data from [`load_input()`].
#' @param results Results from [`process_input()`].
#' @param species Species to be displayed.
scatter_plot <- function(gene_ids, input, results, species) {
if (length(gene_ids) < 1) {
#' @param genes Genes to be displayed.
#' @param distances Distance data to display.
scatter_plot <- function(results, species, genes, distances) {
if (nrow(genes) < 1) {
return(ggplot())
}
species_ids <- species[, id]
data <- merge(
input$genes[id %in% gene_ids, .(id, name)],
input$distances[species %in% species_ids],
genes[, .(id, name)],
distances[species %in% species_ids],
by.x = "id", by.y = "gene"
)
for (gene_id in gene_ids) {
for (gene_id in genes[, id]) {
cluster_species <- unlist(results[gene == gene_id, cluster_species])
data[id == gene_id, in_cluster := species %in% cluster_species]
}
@ -28,7 +29,7 @@ scatter_plot <- function(gene_ids, input, results, species) {
scale_x_discrete(
name = "Species",
breaks = species$id,
labels = species$label
labels = species$name
) +
scale_y_continuous(
name = "Distance to telomeres [Mbp]",