plot_gene_set_haystack {singleCellHaystack}

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.