Tailored feature plot — feature

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