From 75a04592d7b7154240b2a11f889d3da4c7a22126 Mon Sep 17 00:00:00 2001
From: nahid18 <nahidpatwary50@gmail.com>
Date: Sun, 16 Jun 2024 23:33:58 +0600
Subject: [PATCH] feat: clonal prop and plot

---
 NAMESPACE                          |  1 +
 R/plot_clonal_prop_per_sample.R    | 47 ++++++++++++++++++++++++++++++
 R/plot_motif_counts.R              |  8 +++--
 README.md                          |  4 +++
 man/plot_clonal_prop_per_sample.Rd | 26 +++++++++++++++++
 man/plot_motif_counts.Rd           |  2 +-
 6 files changed, 85 insertions(+), 3 deletions(-)
 create mode 100644 R/plot_clonal_prop_per_sample.R
 create mode 100644 man/plot_clonal_prop_per_sample.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 4f6ed56..dc5f292 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,6 +2,7 @@
 
 export("%>%")
 export(get_study)
+export(plot_clonal_prop_per_sample)
 export(plot_motif_counts)
 exportClasses(Basic)
 exportClasses(Clonality)
diff --git a/R/plot_clonal_prop_per_sample.R b/R/plot_clonal_prop_per_sample.R
new file mode 100644
index 0000000..afd6b94
--- /dev/null
+++ b/R/plot_clonal_prop_per_sample.R
@@ -0,0 +1,47 @@
+#' 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 attr_col Character. Attribute column name.
+#'
+#' @return A ggplot2 object representing the clonal proportion per sample 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_sample(clonal_prop, "cmv_status")
+#' }
+plot_clonal_prop_per_sample <- function(data, attr_col) {
+  ggplot2::ggplot(
+    data,
+    ggplot2::aes(
+      x = sample,
+      y = clonality_portion,
+      fill = !!rlang::sym(attr_col)
+    )
+  ) +
+    ggplot2::geom_bar(stat = "identity", position = ggplot2::position_dodge()) +
+    ggplot2::labs(x = "sample", y = "number of clonotypes") +
+    ggplot2::theme_classic() +
+    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)
+    ) +
+    ggplot2::scale_y_continuous(expand = c(0, 0)) +
+    ggplot2::scale_fill_brewer(palette = "Set1", name = attr_col)
+}
diff --git a/R/plot_motif_counts.R b/R/plot_motif_counts.R
index d87b54e..773ff46 100644
--- a/R/plot_motif_counts.R
+++ b/R/plot_motif_counts.R
@@ -10,7 +10,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' proj <- reTCR::get_study(id = "PRJNA473147")
+#' proj <- reTCR::get_study(id="PRJNA473147", attr_col="cmv_status")
 #' reTCR::plot_motif_counts(proj@motif@aa_motif_count, 20)
 #' }
 plot_motif_counts <- function(data, threshold = 60) {
@@ -29,7 +29,11 @@ plot_motif_counts <- function(data, threshold = 60) {
     )
   ) +
     ggplot2::geom_jitter(width = 0.2, size = 3) +
-    ggplot2::labs(x = "Amino acid motif", y = "Count", color = "CMV Status") +
+    ggplot2::labs(
+      x = "Amino acid motif",
+      y = "Count",
+      color = "CMV Status"
+    ) +
     ggplot2::theme_bw() +
     ggplot2::theme(
       axis.text.x = ggplot2::element_text(
diff --git a/README.md b/README.md
index a3a338a..3519aea 100644
--- a/README.md
+++ b/README.md
@@ -106,6 +106,10 @@ print(proj@clonality@pielou)
 # clonal proportion
 print(proj@clonality@clonal_prop)
 
+# plot clonal proportion per sample
+clonal_prop <- proj@clonality@clonal_prop
+reTCR::plot_clonal_prop_per_sample(clonal_prop, "cmv_status")
+
 # relative abundance (in all clonotypes)
 print(proj@clonality@abundance)
 
diff --git a/man/plot_clonal_prop_per_sample.Rd b/man/plot_clonal_prop_per_sample.Rd
new file mode 100644
index 0000000..8d331b8
--- /dev/null
+++ b/man/plot_clonal_prop_per_sample.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot_clonal_prop_per_sample.R
+\name{plot_clonal_prop_per_sample}
+\alias{plot_clonal_prop_per_sample}
+\title{Plot Clonal Proportion per Sample}
+\usage{
+plot_clonal_prop_per_sample(data, attr_col)
+}
+\arguments{
+\item{data}{A data frame containing the clonal proportion per sample.}
+
+\item{attr_col}{Character. Attribute column name.}
+}
+\value{
+A ggplot2 object representing the clonal proportion per sample plot.
+}
+\description{
+This function plots the clonal proportion per sample.
+}
+\examples{
+\dontrun{
+proj <- reTCR::get_study(id="PRJNA473147", attr_col="cmv_status")
+clonal_prop <- proj@clonality@clonal_prop
+reTCR::plot_clonal_prop_per_sample(clonal_prop, "cmv_status")
+}
+}
diff --git a/man/plot_motif_counts.Rd b/man/plot_motif_counts.Rd
index a16683b..107c80b 100644
--- a/man/plot_motif_counts.Rd
+++ b/man/plot_motif_counts.Rd
@@ -19,7 +19,7 @@ This function plots the motif counts.
 }
 \examples{
 \dontrun{
-proj <- reTCR::get_study(id = "PRJNA473147")
+proj <- reTCR::get_study(id="PRJNA473147", attr_col="cmv_status")
 reTCR::plot_motif_counts(proj@motif@aa_motif_count, 20)
 }
 }