dim_plot: Tailored dimensional reduction plot

In andreaskapou/SeuratPipe: Packaging common Seurat analysis tasks

Tailored dimensional reduction plot

Description

This function extends the DimPlot Seurat function by providing additional plotting options.

Usage

dim_plot(
  seu,
  reduction = "umap",
  group.by = "active.ident",
  split.by = NULL,
  ncol = NULL,
  legend.position = "right",
  col_pal = NULL,
  dims_plot = c(1, 2),
  pt.size = 1.4,
  label = FALSE,
  label.size = 7,
  combine = TRUE,
  pt.shape = 21,
  pt.stroke = 0.05,
  pt.alpha = 1,
  ...
)

Arguments

seu	Seurat object (required).
reduction	Which dimensionality reduction to use (required).
group.by	Name of metadata column to group (color) cells by (required).
split.by	Name of a metadata column to split plot by.
ncol	Number of columns for display when combining plots.
legend.position	Position of legend, default "right" (set to "none" for clean plot).
col_pal	Discrete colour palette to use, default is Hue palette (hue_pal) from 'scales' package. Should be of equal length to number of groups in 'group.by'.
dims_plot	Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions.
pt.size	Adjust point size for plotting.
label	Whether to label the clusters in 'plot_reduction' space.
label.size	Sets size of labels.
combine	Combine plots into a single patchworked ggplot object. If FALSE, return a list of ggplot objects
pt.shape	Adjust point shape for plotting.
pt.stroke	Stroke value for each point.
pt.alpha	Adjust alpha value for each point.
...	Additional parameters passed to Seurat's DimPlot.

Value

A ggplot2 object.

Author(s)

C.A.Kapourani [e-mail]

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