Tailored dimensional reduction plot — dim

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

C.A.Kapourani C.A.Kapourani@ed.ac.uk