plot_gene_haystack function

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

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.