Visualizing the detection/expression of a set of genes in a 2D plot

plot_gene_set_haystack(x, ...)

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

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

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

# S3 method for 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.