Modified version of FeatureScatter — FeatureScatter

Create customized FeatureScatter plots with scCustomize defaults.

FeatureScatter_scCustom(
  seurat_object,
  feature1 = NULL,
  feature2 = NULL,
  cells = NULL,
  colors_use = NULL,
  pt.size = NULL,
  group.by = NULL,
  split.by = NULL,
  split_seurat = FALSE,
  shuffle = TRUE,
  aspect_ratio = NULL,
  title_size = 15,
  plot.cor = TRUE,
  num_columns = NULL,
  raster = NULL,
  raster.dpi = c(512, 512),
  ggplot_default_colors = FALSE,
  color_seed = 123,
  ...
)

Arguments

seurat_object: Seurat object name.
feature1: First feature to plot.
feature2: Second feature to plot.
cells: Cells to include on the scatter plot.
colors_use: color for the points on plot.
pt.size: Adjust point size for plotting.
group.by: Name of one or more metadata columns to group (color) cells by (for example, orig.ident). Default is active ident.
split.by: Feature to split plots by (i.e. "orig.ident").
split_seurat: logical. Whether or not to display split plots like Seurat (shared y axis) or as individual plots in layout. Default is FALSE.
shuffle: logical, whether to randomly shuffle the order of points. This can be useful for crowded plots if points of interest are being buried. Default is TRUE.
aspect_ratio: Control the aspect ratio (y:x axes ratio length). Must be numeric value; Default is NULL.
title_size: size for plot title labels. Does NOT apply if split_seurat = TRUE.
plot.cor: Display correlation in plot subtitle (or title if split_seurat = TRUE).
num_columns: number of columns in final layout plot.
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).
ggplot_default_colors: logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
color_seed: random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.
...: Extra parameters passed to FeatureScatter.

Value

A ggplot object

Examples

# \donttest{
library(Seurat)

pbmc_small$sample_id <- sample(c("sample1", "sample2"), size = ncol(pbmc_small), replace = TRUE)

FeatureScatter_scCustom(seurat_object = pbmc_small, feature1 = "nCount_RNA",
feature2 = "nFeature_RNA", split.by = "sample_id")
#> 
#> NOTE: FeatureScatter_scCustom returns split plots as layout of all plots each
#> with their own axes as opposed to Seurat which returns with shared x or y axis.
#> To return to Seurat behvaior set `split_seurat = TRUE`.
#> 
#> -----This message will be shown once per session.-----

# }