Tailored spatial dim plot — spatial_dim

This function adapts the SpatialDimPlot Seurat function by providing additional plotting options.

Usage

spatial_dim_plot(
  seu,
  group.by = "active.ident",
  title = NULL,
  alpha = 0.6,
  pt.size.factor = 1.1,
  crop = FALSE,
  col_pal = NULL,
  legend.position = "top",
  combine = TRUE,
  ...
)

Arguments

seu: Seurat object (required).
group.by: Name of meta.data column to group the data by.
title: Plot title
alpha: Controls opacity of spots. Provide a single alpha value for each plot.
pt.size.factor: Scale the size of the spots.
crop: Crop the plot in to focus on points plotted. Set to FALSE to show entire background image.
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'.
legend.position: Position of legend, default "right" (set to "none" for clean plot).
combine: Combine plots into a single patchworked ggplot object. If FALSE, return a list of ggplot objects
...: Additional parameters passed to Seurat's SpatialDimPlot.

Value

A ggplot2 object.

Author

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