Skip to contents

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