add vizShuffledGrids function

R/visualization.R

@@ -289,6 +289,60 @@ vizGrids <- function(cells, scale,
 
 
 
+#' Visualize grids and clusters after shuffling
+#' 
+#' @description Uses the cells sf object and size of grid to visualize the grids 
+#' and the shuffled null background.
+#' 
+#' @param cells sf object; spatial (x and y) coordinates and celltypes column
+#' @param shuffledList list; cell type labels shuffled at different scales 
+#' (output from makeShuffledCells())
+#' @param scale numeric; size of the scale to plot
+#' @param permutation numeric; the number of the permutation of interest.
+#' @param square boolean; if true, create a squared grid, if false, make 
+#' hexagonal grid (default TRUE)
+#' @param ofInterest character vector; a vector of specific clusters to visualize
+#' @param pointSize numeric; size of points
+#' @param alpha numeric; transparency of points
+#' 
+#' @return plot
+#' 
+#' @examples
+#' \dontrun{
+#' data(slide)
+#' cells <- crawdad::toSF(pos = slide[,c("x", "y")], celltypes = slide$celltypes)
+#' vizAllClusters(cells)
+#' }
+#' 
+#' @export
+vizShuffledGrids <- function(cells, shuffledList, scale, 
+                             permutation = 1, 
+                             square = TRUE,
+                             ofInterest = NULL, pointSize = 1, alpha = 0.5){
+
+  ## define colors to be consistent with the vizCluster function
+  cluster_cols <- rainbow(n = length(unique(cells$celltypes)))
+  names(cluster_cols) <- unique(cells$celltypes)
+  cluster_cols['other'] <- '#E6E6E6'
+
+  ## assing the shuffled labels to the celltypes column
+  shuffled_labels <- shuffledList[[as.character(scale)]][[as.character(permutation)]]
+  cells$celltypes <- as.factor(shuffled_labels)
+  ## determine the total number of permutations to perform the offsetting
+  totalPermutations <- length(shuffledList[[1]])
+
+  ## use vizGrids to plot
+  vizGrids(cells = cells, scale = scale, 
+           permutation = permutation, totalPermutations = totalPermutations,
+           square = square,
+           ofInterest = ofInterest, pointSize = pointSize, alpha = alpha) +
+    ## NA to gray
+    ggplot2::scale_color_manual(values = cluster_cols, na.value = "#E6E6E6")
+
+}
+
+
+
 #' Plot trends with ggplot2
 #' 
 #' @description The input data.frame should be the results list from `findTrends()` that has been melted into a data.frame using `meltResultsList()`.