From cbedbe7fcf45e7b1c02a7732b73157ec580af5fc Mon Sep 17 00:00:00 2001
From: Shreya Rao <shreya.rao@wimr.org.au>
Date: Wed, 18 Dec 2024 13:36:14 +0530
Subject: [PATCH] plotImage function

---
 NAMESPACE        |  4 +++
 R/plotImage.R    | 91 ++++++++++++++++++++++++++++++++++++++++++++++++
 man/plotImage.Rd | 42 ++++++++++++++++++++++
 3 files changed, 137 insertions(+)
 create mode 100644 R/plotImage.R
 create mode 100644 man/plotImage.Rd

diff --git a/NAMESPACE b/NAMESPACE
index b866fd5..42d8604 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -5,11 +5,15 @@ export(colTest)
 export(convPairs)
 export(getPairwise)
 export(getProp)
+export(plotImage)
 export(signifPlot)
 export(spicy)
 export(spicyBoxPlot)
 export(topPairs)
 exportClasses(SpicyResults)
+import(SpatialExperiment)
+import(SummarizedExperiment)
+import(dplyr)
 import(ggh4x)
 import(ggplot2)
 import(ggthemes)
diff --git a/R/plotImage.R b/R/plotImage.R
new file mode 100644
index 0000000..36d15ea
--- /dev/null
+++ b/R/plotImage.R
@@ -0,0 +1,91 @@
+#' Plots an image with specified from and to cell types.
+#' 
+#' @param cells A SummarizedExperiment object.
+#' @param imageToPlot The ID of the image to be plotted.
+#' @param from The "from" cell type.
+#' @param to The "to" cell type.
+#' @param imageID The name of the imageID column in the SummarizedExperiment object.
+#' @param cellType The name of the cellType column in the SummarizedExperiment object. 
+#' @param spatialCoords The names of the spatialCoords column if using a SingleCellExperiment.
+#' 
+#' @return A ggplot object.
+#' 
+#' @examples
+#' data("diabetesData")
+#' plotImage(diabetesData, "A09", from = "acinar", to = "alpha")
+#' 
+#' @export
+#' @import dplyr 
+#' @import ggplot2 
+#' @import SummarizedExperiment
+#' @import SpatialExperiment
+plotImage = function(cells, 
+                     imageToPlot, 
+                     from,
+                     to,
+                     imageID = "imageID", 
+                     cellType = "cellType",
+                     spatialCoords = c("x", "y")) {
+  
+  if (!is(cells, "SummarizedExperiment")) {
+    stop(paste("Please provide a SummarizedExperiment object as input."))
+  }
+  
+  if (!imageID %in% colnames(colData(cells))) {
+    stop(paste0(imageID, " not found in colData."))
+  }
+  
+  if (!imageToPlot %in% unique(cells[[imageID]])) {
+    stop(paste0("imageToPlot not found in ", imageID, " column."))
+  }
+  
+  if (!cellType %in% colnames(colData(cells))) {
+    stop(paste0(cellType, " not found in colData."))
+  }
+  
+  if (!all(spatialCoords %in% colnames(colData(cells)))) {
+    stop(paste0(spatialCoords, " not found in colData."))
+  }
+  
+  if (length(spatialCoords) != 2) {
+    stop(paste("Please provide x and y coordinates columns."))
+  }
+  
+  if (!all(c(from, to) %in% unique(colData(cells)[[cellType]]))) {
+    stop("from and/or to cell types not found in data.")
+  }
+  
+  if (class(cells) == "SingleCellExperiment") {
+    cells = SpatialExperiment(assays = assays(cells), 
+                              colData = colData(cells), 
+                              rowData = rowData(cells))
+    spatialCoords(cells) = as.matrix(colData(cells)[, c(spatialCoords[1], spatialCoords[2])])
+  }
+  
+  # filter for specific image
+  subset = cells[, colData(cells)[[imageID]] == imageToPlot]
+  
+  coords = spatialCoords(subset) |> as.data.frame()
+  cData = data.frame(x = coords[["x"]],
+                     y = coords[["y"]],
+                     cellType = subset[[cellType]])
+  
+  cData[[cellType]] = as.character(cData[[cellType]])
+  cData = cData |> mutate(cellTypeNew = 
+                            ifelse(cellType %in% c(from, to), cellType, "Other"))
+  
+  
+  pal = setNames(c("#d6b11c", "#850f07"), c(from, to))
+  
+  ggplot() +
+    stat_density_2d(data = cData, aes(x = x, y = y, fill = after_stat(density)), 
+                    geom = "raster", 
+                    contour = FALSE) +
+    geom_point(data = cData |> filter(cellTypeNew != "Other"),
+               aes(x = x, y = y, colour = cellTypeNew), size = 1) +
+    scale_color_manual(values = pal) +
+    scale_fill_distiller(palette = "Blues", direction = 1) +
+    theme_classic() +
+    labs(title = paste0(imageID, ": ", imageToPlot),
+         color = cellType)
+}
\ No newline at end of file
diff --git a/man/plotImage.Rd b/man/plotImage.Rd
new file mode 100644
index 0000000..b5f9f91
--- /dev/null
+++ b/man/plotImage.Rd
@@ -0,0 +1,42 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plotImage.R
+\name{plotImage}
+\alias{plotImage}
+\title{Plots an image with specified from and to cell types.}
+\usage{
+plotImage(
+  cells,
+  imageToPlot,
+  from,
+  to,
+  imageID = "imageID",
+  cellType = "cellType",
+  spatialCoords = c("x", "y")
+)
+}
+\arguments{
+\item{cells}{A SummarizedExperiment object.}
+
+\item{imageToPlot}{The ID of the image to be plotted.}
+
+\item{from}{The "from" cell type.}
+
+\item{to}{The "to" cell type.}
+
+\item{imageID}{The name of the imageID column in the SummarizedExperiment object.}
+
+\item{cellType}{The name of the cellType column in the SummarizedExperiment object.}
+
+\item{spatialCoords}{The names of the spatialCoords column if using a SingleCellExperiment.}
+}
+\value{
+A ggplot object.
+}
+\description{
+Plots an image with specified from and to cell types.
+}
+\examples{
+data("diabetesData")
+plotImage(diabetesData, "A09", from = "acinar", to = "alpha")
+
+}