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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