plot_gene_haystack_raw() R function from [singleCellHaystack]

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


plot_gene_haystack_raw(
  x,
  y,
  gene,
  expression,
  detection = NULL,
  high.resolution = FALSE,
  point.size = 1,
  order.by.signal = FALSE
)

x: x-axis coordinates of cells in a 2D representation (e.g. resulting from PCA or t-SNE)
y: y-axis coordinates of cells in a 2D representation
gene: name of a gene that is present in the input expression data, or a numerical index
expression: a logical/numerical matrix showing detection/expression of genes (rows) in cells (columns)
detection: an optional logical matrix showing detection of genes (rows) in cells (columns). If left as NULL, the density distribution of the gene is not plotted.
high.resolution: logical (default: FALSE). If set to TRUE, the density plot will be of a higher resolution
point.size: numerical value to set size of points in plot. Default is 1.
order.by.signal: If TRUE, cells with higher signal will be put on the foreground in the plot. Default is FALSE.

A plot

Useful links