From 34802cda8ee91bfa2b39f65536387e7511de860d Mon Sep 17 00:00:00 2001
From: Michael Morley <mmorley@pennmedicine.upenn.edu>
Date: Thu, 14 Oct 2021 15:56:01 -0400
Subject: [PATCH] Added sampleBarGraph function

---
 DESCRIPTION           |  2 +-
 NAMESPACE             |  1 +
 R/Plotting.R          | 37 +++++++++++++++++++++++++++++++++++++
 man/sampleBarGraph.Rd | 18 ++++++++++++++++++
 4 files changed, 57 insertions(+), 1 deletion(-)
 create mode 100644 man/sampleBarGraph.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 651ab88..7d5181b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -8,4 +8,4 @@ Maintainer: Who to complain to <yourfault@somewhere.net>
 Description: Functions to run Seurat, slingshot, monocle and other scRNA packages on single cell data
 License: What license is it under?
 LazyData: TRUE
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
diff --git a/NAMESPACE b/NAMESPACE
index 53b7fe3..8968fbf 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -27,6 +27,7 @@ export(plotLineangeGene)
 export(processExper)
 export(runPseudoTimeDGE)
 export(runSlingshot)
+export(sampleBarGraph)
 export(setSDS)
 import(ComplexHeatmap)
 import(DoubletFinder)
diff --git a/R/Plotting.R b/R/Plotting.R
index 41e481c..315b53b 100644
--- a/R/Plotting.R
+++ b/R/Plotting.R
@@ -1,4 +1,41 @@
 
+#'Plot a stacked bar graph of per Sample contribtion
+#' @param object Seurat object
+#' @param group.by Variable for x axis typicall cluster or celltype
+#' @param cols Color palette for grouping variable
+#' @export
+
+sampleBarGraph <- function(object,group.by=NULL,col=NULL){
+  if(is.null(group.by)){
+    print("group.by cannot be null")
+    exit()
+  }
+  if(is.null(object$sample)){
+    print("Cannot find Sample field in meta data")
+    exit()
+  }
+
+
+  p <- object@meta.data %>%
+    group_by(sample,!!sym(group.by)) %>%
+    summarise(n = n()) %>%
+    mutate(pct = n / sum(n))  %>%
+    ggplot(.,aes(x=!!sym(group.by),y=pct,fill=sample)) +
+    geom_bar(position="fill", stat="identity")  +
+    scale_y_continuous(labels = scales::percent_format()) +
+    scale_fill_manual(values=col) +
+    theme_bw() + theme(legend.position = 'bottom')
+
+  if(!is.null(col)){
+    p <- p + scale_fill_manual(values=col)
+  }
+  p
+
+
+}
+
+
+
 #'Plot Pairwise PCA plots.
 #' @param object Seurat object
 #' @param dims Compute N PC dims
diff --git a/man/sampleBarGraph.Rd b/man/sampleBarGraph.Rd
new file mode 100644
index 0000000..5914f7d
--- /dev/null
+++ b/man/sampleBarGraph.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Plotting.R
+\name{sampleBarGraph}
+\alias{sampleBarGraph}
+\title{Plot a stacked bar graph of per Sample contribtion}
+\usage{
+sampleBarGraph(object, group.by = NULL, col = NULL)
+}
+\arguments{
+\item{object}{Seurat object}
+
+\item{group.by}{Variable for x axis typicall cluster or celltype}
+
+\item{cols}{Color palette for grouping variable}
+}
+\description{
+Plot a stacked bar graph of per Sample contribtion
+}