new functions

R/plot_cluster_thresholds.R

+#' Plot cluster counts across similarity thresholds
+#'
+#' This function creates a plot of cluster thresholds based on a given table of cluster counts
+#' and a defined plateau.
+#'
+#' @param clus_counts_tbl A data frame containing the cluster counts. It should have two columns:
+#'   - threshold: The threshold values.
+#'   - cluster_number: The corresponding number of clusters.
+#'
+#' @param plateaus A named numeric vector containing the plateau information. It should have the following
+#'   elements:
+#'   - plateau_start: The starting threshold value of the plateau.
+#'   - plateau_end: The ending threshold value of the plateau.
+#'   - cluster_number: The number of clusters within the plateau.
+#'
+#' @return A plot of cluster thresholds with highlighted plateaus.
+#'
+#' @examples
+#' clus_counts_tbl <- data.frame(
+#'   threshold = c(0.1, 0.2, 0.3, 0.4, 0.5),
+#'   cluster_number = c(7, 6, 6, 5, 4)
+#' )
+#'
+#' plateaus <- c(
+#'   plateau_start = 0.2,
+#'   plateau_end = 0.3,
+#'    cluster_number = 6
+#' )
+#'
+#' plot_cluster_thresholds(clus_counts_tbl, plateaus)
+#'
+#'
+#' @export
+
+plot_cluster_thresholds <- function(clus_counts_tbl, plateaus) {
+  ggplot(clus_counts_tbl, aes(x = threshold, y = cluster_number)) +
+    geom_rect(aes(xmin = plateaus['plateau_start'],
+                  xmax = plateaus['plateau_end'], ymin = 0,
+                  ymax = max(cluster_number)), fill = 'lightblue') +
+    geom_point() +
+    annotate('text', x = plateaus['plateau_start'],
+             y = max(clus_counts_tbl$cluster_number)/2,
+             label = paste('Clusters:', plateaus['cluster_number']),
+             hjust = 0) +
+    annotate('text', x = plateaus['plateau_start'],
+             y = max(clus_counts_tbl$cluster_number)/2.5,
+             label = paste(
+               'Threshold:', plateaus['plateau_start'],
+               'to', plateaus['plateau_end']),
+             hjust = 0)
+}

R/str_pad_to_max.R

+#' Pad string to longest length
+#'
+#' Pads each element in a character vector to the length of the longest element in the vector.
+#'
+#' @param vec The character vector to be padded.
+#' @param ... Additional arguments to be passed to `str_pad`.
+#'
+#' @return The character vector with each element padded to the maximum length.
+#'
+#' @examples
+#' str_pad_to_max(c("hello", "world", "foo", "bar", "x"))
+#'
+#' @importFrom stringr str_pad str_length
+#'
+#' @export
+str_pad_to_max <- function(vec = c(), ...){
+  str_pad(vec, max(str_length(vec)), ...)
+}