Meta Highlight Plot — Cell_Highlight

Create Plot with meta data variable of interest highlighted

Cell_Highlight_Plot(
  seurat_object,
  cells_highlight,
  highlight_color = NULL,
  background_color = "lightgray",
  pt.size = NULL,
  aspect_ratio = NULL,
  figure_plot = FALSE,
  raster = NULL,
  raster.dpi = c(512, 512),
  label = FALSE,
  split.by = NULL,
  split_seurat = FALSE,
  reduction = NULL,
  ggplot_default_colors = FALSE,
  ...
)

Arguments

seurat_object: Seurat object name.
cells_highlight: Cell names to highlight in named list.
highlight_color: Color to highlight cells.
background_color: non-highlighted cell colors (default is "lightgray")..
pt.size: point size for both highlighted cluster and background.
aspect_ratio: Control the aspect ratio (y:x axes ratio length). Must be numeric value; Default is NULL.
figure_plot: logical. Whether to remove the axes and plot with legend on left of plot denoting axes labels. (Default is FALSE). Requires split_seurat = TRUE.
raster: Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.
raster.dpi: Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).
label: Whether to label the highlighted meta data variable(s). Default is FALSE.
split.by: Variable in @meta.data to split the plot by.
split_seurat: logical. Whether or not to display split plots like Seurat (shared y axis) or as individual plots in layout. Default is FALSE.
reduction: Dimensionality Reduction to use (if NULL then defaults to Object default).
ggplot_default_colors: logical. If highlight_color = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
...: Extra parameters passed toDimPlot.

Value

A ggplot object

Examples

library(Seurat)

# Creating example non-overlapping vectors of cells
MS4A1 <- WhichCells(object = pbmc_small, expression = MS4A1 > 4)
GZMB <- WhichCells(object = pbmc_small, expression = GZMB > 4)

# Format as named list
cells <- list("MS4A1" = MS4A1,
              "GZMB" = GZMB)

Cell_Highlight_Plot(seurat_object = pbmc_small, cells_highlight = cells)