plot_gene_haystack_raw: Visualizing the detection/expression of a gene in a 2D plot

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

Visualizing the detection/expression of a gene in a 2D plot

Description

Visualizing the detection/expression of a gene in a 2D plot

Usage

plot_gene_haystack_raw(
  x,
  y,
  gene,
  expression,
  detection = NULL,
  high.resolution = FALSE,
  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
gene	name of a gene that is present in the input expression data, or a numerical index
expression	a logical/numerical matrix showing detection/expression of genes (rows) in cells (columns)
detection	an optional logical matrix showing detection of genes (rows) in cells (columns). If left as NULL, the density distribution of the gene is not plotted.
high.resolution	logical (default: FALSE). If set to TRUE, the density plot will be of a higher 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

singleCellHaystack documentation built on June 22, 2024, 11:57 a.m.