Tailored spatial feature plot — spatial_feature

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

Usage

spatial_feature_plot(
  seu,
  features = "nFeature_Spatial",
  title = NULL,
  alpha = c(0.1, 0.9),
  pt.size.factor = 1.1,
  ncol = NULL,
  max.cutoff = "q98",
  min.cutoff = NA,
  crop = FALSE,
  col_pal = "inferno",
  legend.position = "top",
  combine = TRUE,
  ...
)

Arguments

seu: Seurat object (required).
features: Vector of features to plot.
title: Plot title
alpha: Controls opacity of spots. Provide as a vector specifying the min and max range of values (between 0 and 1).
pt.size.factor: Scale the size of the spots.
ncol: Number of columns for display when having multiple features.
max.cutoff: Vector of maximum cutoff values for each feature, may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10').
min.cutoff: Vector of minimum cutoff values for each feature, may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10').
crop: Crop the plot in to focus on points plotted. Set to FALSE to show entire background image.
col_pal: Continuous colour palette to use from viridis package, default "inferno".
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 SpatialFeaturePlot.

Value

A ggplot2 object.

Author

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