feature_plot: Tailored feature plot

In andreaskapou/SeuratPipe: Packaging common Seurat analysis tasks

Tailored feature plot

Description

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(s)

C.A.Kapourani [e-mail]

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