Subset dim plot — subset_dim

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

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