subset_dim_plot: Subset dim plot

In andreaskapou/SeuratPipe: Packaging common Seurat analysis tasks

Subset dim plot

Description

This function splits the dim plots according to a grouping variable defined in subset.by. The main difference is that the whole dataset is also shown in the background as smaller points.

Usage

subset_dim_plot(
  seu,
  subset.by,
  reduction = "umap",
  ncol = NULL,
  col_pal = NULL,
  pt.size = 2,
  pt.stroke = 0.05,
  pt.shape = 21,
  pt.alpha = 1,
  back.pt.size = 0.5,
  back.pt.alpha = 0.1,
  back.pt.color = "grey",
  combine = TRUE,
  dims_plot = c(1, 2),
  ...
)

Arguments

seu	Seurat object
subset.by	Metadata column whose unique values will generate split dim plots.
reduction	Dimensionality reduction to use.
ncol	Number of columns for display when having multiple features.
col_pal	Discrete colour palette to use.
pt.size	Adjust point size for plotting.
pt.stroke	Stroke value for each point.
pt.shape	Adjust point shape for plotting.
pt.alpha	Adjust alpha value for each point.
back.pt.size	Adjust background point size for plotting.
back.pt.alpha	Adjust opacity for background points.
back.pt.color	Colour for background points.
combine	Combine plots into a single patchworked ggplot object. If FALSE, return a list of ggplot objects
dims_plot	Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions.
...	Additional parameters passed to ggplot2::geom_point.

Value

A ggplot2 object.

Author(s)

C.A.Kapourani [e-mail]

andreaskapou/SeuratPipe documentation built on Nov. 22, 2022, 4:16 p.m.