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

In alexisvdb/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(x, ...)

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

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

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

## S3 method for class 'Seurat'
plot_gene_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.

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