spatial_feature_plot: Tailored spatial feature plot

In andreaskapou/SeuratPipe: Packaging common Seurat analysis tasks

Tailored spatial feature plot

Description

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(s)

C.A.Kapourani [e-mail]

andreaskapou/SeuratPipe documentation built on Nov. 22, 2022, 4:16 p.m.