Skip to contents

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

Usage

feature_plot(
  seu,
  reduction = "umap",
  features = "nFeature_RNA",
  max.cutoff = "q98",
  min.cutoff = NA,
  ncol = NULL,
  legend.position = "right",
  col_pal = NULL,
  dims_plot = c(1, 2),
  pt.size = 1.4,
  combine = TRUE,
  ...
)

Arguments

seu

Seurat object (required).

reduction

Which dimensionality reduction to use (required).

features

Vector of features to plot.

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').

ncol

Number of columns for display when having multiple features.

legend.position

Position of legend, default "right" (set to "none" for clean plot).

col_pal

Continuous colour palette to use, default "RdYlBu".

dims_plot

Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions.

pt.size

Adjust point size for plotting.

combine

Combine plots into a single patchworked ggplot object. If FALSE, return a list of ggplot objects

...

Additional parameters passed to Seurat's FeaturePlot.

Value

A ggplot2 object.

Author

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