plot_gene_set_haystack_raw: Visualizing the detection/expression of a set of genes in a...

In alexisvdb/singleCellHaystack: A Universal Differential Expression Prediction Tool for Single-Cell and Spatial Genomics Data

Visualizing the detection/expression of a set of genes in a 2D plot

Description

Visualizing the detection/expression of a set of genes in a 2D plot

Usage

plot_gene_set_haystack_raw(
  x,
  y,
  genes = NA,
  detection,
  high.resolution = TRUE,
  point.size = 1,
  order.by.signal = FALSE
)

Arguments

x	x-axis coordinates of cells in a 2D representation (e.g. resulting from PCA or t-SNE)
y	y-axis coordinates of cells in a 2D representation
genes	Gene names that are present in the input expression data, or a numerical indeces. If NA, all genes will be used.
detection	a logical matrix showing detection of genes (rows) in cells (columns)
high.resolution	logical (default: TRUE). If set to FALSE, the density plot will be of a lower resolution
point.size	numerical value to set size of points in plot. Default is 1.
order.by.signal	If TRUE, cells with higher signal will be put on the foreground in the plot. Default is FALSE.

Value

A plot

alexisvdb/singleCellHaystack documentation built on Jan. 17, 2024, 10:45 a.m.