R/nice_spatial_dim_plot.R

In mvhunter1/mvhspatialplots: Some improved functions for analysis of ST and GSEA data.

#' @title nice_spatial_dim_plot
#' @description nicer looking version of the Seurat function SpatialDimPlot.
#' @param seurat_obj Seurat object.
#' @param group.by what to colour the points by, usually a column in the Seurat object metadata.
#' @param im_alpha set to 1 to plot the tissue image, 0 otherwise.
#' @param pt.size size of plotted points on spatial array.
#' @param stroke linewidth to outline plotted points in black (default = no outline).
#' @param cols optional: vector of colours for each plotted group.
#' @param label if T, will label groups with text on plot.
#' @param show_legend if T, will include the legend but won't label points w/text on plot.
#' @export
#' @return SpatialPlot.

nice_spatial_dim_plot <- function(seurat_obj, group.by, im_alpha = 0, pt.size = 1.4, stroke = 0, cols = NULL, label = F, show_legend = T) {

  if (label) {
    plot <- Seurat::SpatialPlot(seurat_obj,
                                group.by = group.by,
                                image.alpha = im_alpha,
                                pt.size.factor = pt.size,
                                stroke = stroke,
                                cols = cols,
                                label = T) + NoLegend()
  } else {
    plot <- Seurat::SpatialPlot(seurat_obj,
                                group.by = group.by,
                                image.alpha = im_alpha,
                                pt.size.factor = pt.size,
                                stroke = stroke,
                                cols = cols,
                                label = F)
  }
  return(plot)
}