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

In 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(x, ...)

## S3 method for class 'matrix'
plot_gene_set_haystack(x, dim1 = 1, dim2 = 2, ...)

## S3 method for class 'data.frame'
plot_gene_set_haystack(x, dim1 = 1, dim2 = 2, ...)

## S3 method for class 'SingleCellExperiment'
plot_gene_set_haystack(
  x,
  dim1 = 1,
  dim2 = 2,
  assay = "counts",
  coord = "TSNE",
  ...
)

## S3 method for class 'Seurat'
plot_gene_set_haystack(
  x,
  dim1 = 1,
  dim2 = 2,
  assay = "RNA",
  slot = "data",
  coord = "tsne",
  ...
)

Arguments

x	a matrix or other object from which coordinates of cells can be extracted.
...	further parameters passed to plot_gene_haystack_raw().
dim1	column index or name of matrix for x-axis coordinates.
dim2	column index or name of matrix for y-axis coordinates.
assay	name of assay data for Seurat method.
coord	name of coordinates slot for specific methods.
slot	name of slot for assay data for Seurat method.

singleCellHaystack documentation built on Dec. 28, 2022, 1:29 a.m.