This function plots feature expression in reduced dimensions using the FeaturePlot function from the Seurat package.
Usage
sn_plot_feature(
object,
features,
reduction = NULL,
label = label,
split_by = NULL,
label_size = 8 * 0.36,
pt_size = 1,
slot = "data",
max_cutoff = NA,
raster = TRUE,
seed = 717,
title = NULL,
legend_title = NULL,
show_legend = TRUE,
show_axis = TRUE,
show_border = TRUE,
palette = "YlOrRd",
direction = 1,
...
)Arguments
- object
A Seurat object containing the data to plot.
- features
A character vector of feature names to plot.
- reduction
A character string specifying the dimensionality reduction to use (e.g., "PCA", "UMAP", "tSNE"). Defaults to NULL.
- label
A character vector specifying the labels to use for each cell group. Defaults to label.
- split_by
A character vector specifying the cell groups to split the plot by. Defaults to NULL.
- label_size
A numeric value specifying the size of the labels. Defaults to 8 * 0.36.
- pt_size
A numeric value specifying the size of the points. Defaults to 1.
- slot
A character string specifying which slot in the Seurat object to use (e.g., "data", "scale.data", "integrated"). Defaults to "data".
- max_cutoff
A numeric value specifying the maximum expression cutoff. Defaults to NA.
- raster
A logical value specifying whether to use raster graphics. Defaults to TRUE.
- seed
An integer value specifying the random seed. Defaults to 717.
- title
A character string specifying the plot title. Defaults to NULL.
- legend_title
A character string specifying the legend title. Defaults to NULL.
- show_legend
A logical value specifying whether to show the legend. Defaults to TRUE.
- show_axis
A logical value specifying whether to show the plot axis. Defaults to TRUE.
- show_border
A logical value specifying whether to show the plot border. Defaults to TRUE.
- palette
A character string specifying the color palette to use. Defaults to "YlOrRd".
- direction
A numeric value specifying the direction of the color palette. Defaults to 1.
- ...
Additional parameters to pass to FeaturePlot.
Examples
if (FALSE) { # \dontrun{
sn_plot_feature(x = mySeuratObject, features = c("CD3D", "CD8A", "CD4"), reduction = "UMAP")
} # }