feat: clonal prop per group plot

NAMESPACE

@@ -2,6 +2,7 @@
 
 export("%>%")
 export(get_study)
+export(plot_clonal_prop_per_group)
 export(plot_clonal_prop_per_sample)
 export(plot_motif_counts)
 exportClasses(Basic)

R/plot_clonal_prop_per_group.R

@@ -0,0 +1,47 @@
+#' Plot clonal proportion per group
+#'
+#' This function plots the clonal proportion per group.
+#'
+#' @param data A data frame of clonal proportion per group.
+#' @param attr_col Character. Attribute column name.
+#'
+#' @return A ggplot2 plot of clonal proportion per group plot.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' proj <- reTCR::get_study(id = "PRJNA473147", attr_col = "cmv_status")
+#' clonal_prop <- proj@clonality@clonal_prop
+#' reTCR::plot_clonal_prop_per_group(clonal_prop, "cmv_status")
+#' }
+plot_clonal_prop_per_group <- function(data, attr_col) {
+  data[[attr_col]] <- as.factor(data[[attr_col]])
+  ggplot2::ggplot(
+    data,
+    ggplot2::aes_string(
+      x = attr_col,
+      y = "clonality_portion"
+    )
+  ) +
+    ggplot2::geom_violin(trim = FALSE, fill = "skyblue", alpha = 0.5) +
+    ggplot2::geom_boxplot(outlier.shape = NA, width = 0.1, alpha = 0.7) +
+    ggplot2::geom_jitter(width = 0, height = 0.1, size = 1.5, alpha = 0.6) +
+    ggplot2::theme_classic() +
+    ggplot2::labs(x = attr_col, y = "number of clonotypes") +
+    ggplot2::theme(
+      axis.text.x = ggplot2::element_text(
+        angle = 90, vjust = 0.5, hjust = 1, size = 10
+      ),
+      axis.text.y = ggplot2::element_text(
+        size = 12,
+        margin = ggplot2::margin(l = 10)
+      ),
+      axis.title.x = ggplot2::element_text(
+        size = 14,
+        margin = ggplot2::margin(t = 10)
+      ),
+      axis.title.y = ggplot2::element_text(size = 14),
+      legend.title = ggplot2::element_text(size = 14),
+      legend.text = ggplot2::element_text(size = 12)
+    )
+}

R/plot_clonal_prop_per_sample.R

@@ -1,11 +1,11 @@
-#' Plot Clonal Proportion per Sample
+#' Plot clonal proportion per sample
 #'
 #' This function plots the clonal proportion per sample.
 #'
-#' @param data A data frame containing the clonal proportion per sample.
+#' @param data A data frame of clonal proportion per sample.
 #' @param attr_col Character. Attribute column name.
 #'
-#' @return A ggplot2 object representing the clonal proportion per sample plot.
+#' @return A ggplot2 plot of clonal proportion per sample plot.
 #' @export
 #'
 #' @examples

README.md

@@ -104,12 +104,15 @@ print(proj@clonality@least_clonotype)
 print(proj@clonality@pielou)
 
 # clonal proportion
-print(proj@clonality@clonal_prop)
+clonal_prop <- proj@clonality@clonal_prop
+print(clonal_prop)
 
 # plot clonal proportion per sample
-clonal_prop <- proj@clonality@clonal_prop
 reTCR::plot_clonal_prop_per_sample(clonal_prop, "cmv_status")
 
+# plot clonal proportion per group
+reTCR::plot_clonal_prop_per_group(clonal_prop, "cmv_status")
+
 # relative abundance (in all clonotypes)
 print(proj@clonality@abundance)