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

plot_gene_set_haystack_raw(
  x,
  y,
  genes = NA,
  detection,
  high.resolution = TRUE,
  point.size = 1,
  order.by.signal = FALSE
)

Arguments

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
genes: Gene names that are present in the input expression data, or a numerical indeces. If NA, all genes will be used.
detection: a logical matrix showing detection of genes (rows) in cells (columns)
high.resolution: logical (default: TRUE). If set to FALSE, the density plot will be of a lower 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