scCustomize (version 3.0.0)

Cell_Highlight_Plot: Meta Highlight Plot

Description

Create Plot with meta data variable of interest highlighted

Usage

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,
  ...
)

Value

A ggplot object

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.

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)