plot_spot_enrichments: this function plot spatial patterns of enriched GO terms to...

In tmirus/TTT: What the Package Does (One Line, Title Case)

Description

this function plot spatial patterns of enriched GO terms to pdf

Usage

plot_spot_enrichments(
  enrichment.mat,
  term.names = NULL,
  ids,
  plot.params = list(nx = 35, ny = 33, ox = 0, oy = 0),
  img = NULL,
  filename = "spot_enrichments.pdf",
  output.path = "./"
)

Arguments

enrichment.mat	numeric matrix of enrichment p-values (terms x spots) as returned by test_spot_enrichment or filter_spot_enrichments
term.names	character vector containing full term names for GO ids in enrichment.mat
ids	barcode data frame assigning spots to x and y coordinates (see process_input)
plot.params	list of parameters needed for good spatial visualization as returned by plot_adjustment
img	EBImage image object the information will be plotted on; default NULL
filename	character, name of the pdf; default "spot_enrichments.pdf"
output.path	character specifying output directory; default "./"

tmirus/TTT documentation built on April 17, 2021, 11:04 p.m.