feat: reads group abundance

NAMESPACE

@@ -4,8 +4,9 @@ export("%>%")
 export(get_study)
 export(plot_clonal_prop_per_group)
 export(plot_clonal_prop_per_sample)
+export(plot_clonotype_abundance)
 export(plot_motif_counts)
-export(plot_relative_abundance)
+export(plot_reads_group_abundance)
 exportClasses(Basic)
 exportClasses(Clonality)
 exportClasses(Diversity)

R/plot_relative_abundance.R → R/plot_clonotype_abundance.R

@@ -10,11 +10,12 @@
 #'
 #' @examples
 #' \dontrun{
-#' proj <- reTCR::get_study(id = "PRJNA473147", attr_col = "cmv_status")
-#' reTCR::plot_relative_abundance(proj@clonality@abundance)
+#' proj <- reTCR::get_study(id="PRJNA473147", attr_col="cmv_status")
+#' reTCR::plot_clonotype_abundance(proj@clonality@abundance)
 #' }
-plot_relative_abundance <- function(data) {
-  label_order <- c("Hyperexpanded", "Large", "Medium", "Small", "Rare")
+plot_clonotype_abundance <- function(data) {
+  label_order <- unique(data$clonotype_group)
+  colors <- c("#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00")
 
   ggplot2::ggplot(
     data,
@@ -26,7 +27,7 @@ plot_relative_abundance <- function(data) {
       color = NA
     ) +
     ggplot2::scale_fill_manual(
-      values = c("#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00"),
+      values = colors,
       breaks = label_order
     ) +
     ggplot2::labs(x = "sample", y = "clonotype frequency") +

R/plot_reads_group_abundance.R

@@ -0,0 +1,63 @@
+#' Plot reads group abundance for top 100 clonotypes
+#'
+#' This function plots reads group abundance for top 100 clonotypes.
+#'
+#' @param data A data frame of relative abundance for top 100 clonotypes.
+#' @param attr_col Character. Attribute column name.
+#'
+#' @return A ggplot2 plot of reads group abundance for top 100 clonotypes.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' proj <- reTCR::get_study(id = "PRJNA473147", attr_col = "cmv_status")
+#' reTCR::plot_reads_group_abundance(proj@clonality@abundance_top)
+#' }
+plot_reads_group_abundance <- function(data) {
+  label_order <- unique(data$reads_group)
+  colors <- c("#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00")
+
+  df_counts <- data %>%
+    dplyr::filter(reads_group != "None") %>%
+    dplyr::group_by(sample, reads_group) %>%
+    dplyr::summarize(count = dplyr::n()) %>%
+    dplyr::ungroup()
+
+  ggplot2::ggplot(
+    df_counts,
+    ggplot2::aes(
+      x = sample,
+      y = count,
+      fill = reads_group
+    )
+  ) +
+    ggplot2::geom_bar(position = "stack", stat = "identity", width = 0.7) +
+    ggplot2::scale_fill_manual(
+      values = colors,
+      breaks = label_order,
+      name = "reads_group"
+    ) +
+    ggplot2::labs(x = "sample", y = "number of clonotypes") +
+    ggplot2::theme_minimal() +
+    ggplot2::theme(
+      axis.text.x = ggplot2::element_text(
+        angle = 90, vjust = 0.5, hjust = 1, size = 10
+      ),
+      axis.text.y = ggplot2::element_text(size = 10),
+      axis.title = ggplot2::element_text(size = 14),
+      legend.title = ggplot2::element_blank(),
+      legend.text = ggplot2::element_text(size = 12),
+      legend.position = "right",
+      panel.grid.major = ggplot2::element_blank(),
+      panel.grid.minor = ggplot2::element_blank(),
+      axis.line = ggplot2::element_line(color = "black"),
+      axis.text = ggplot2::element_text(margin = ggplot2::margin(t = 10)),
+      axis.ticks = ggplot2::element_line(color = "black", size = 0.3),
+      strip.background = ggplot2::element_blank(),
+      strip.text = ggplot2::element_text(size = 12)
+    ) +
+    ggplot2::scale_x_discrete(
+      labels = function(x) stringr::str_wrap(x, width = 10)
+    ) +
+    ggplot2::scale_y_continuous(expand = c(0, 0))
+}

README.md

@@ -119,11 +119,14 @@ reTCR::plot_clonal_prop_per_group(clonal_data, "cmv_status")
 print(proj@clonality@abundance)
 
 # plot relative abundance in all clonotypes
-reTCR::plot_relative_abundance(proj@clonality@abundance)
+reTCR::plot_clonotype_abundance(proj@clonality@abundance)
 
 # relative abundance (in top 100 clonotypes)
 print(proj@clonality@abundance_top)
 
+# plot reads group abbundance in top 100 clonotypes
+reTCR::plot_reads_group_abundance(proj@clonality@abundance_top)
+
 # relative abundance (in rare clonotypes)
 print(proj@clonality@abundance_rare)
 ```