Hello, I used the GRaNIE package I wanted to color my GRN network, based of the communities, but I mentioned that the visualizeGRN function's arguments in the Reference Manual and actual package is not the same (see the code below). The nCommunitiesMax argument is absent in this function from the actual package version, and it leads to error when I try to color the GRN network by community. Please, add the nCommunitiesMax argument to the list of the visualizeGRN arguments (maybe it's just a typo?).

## Reference Manual version
visualizeGRN(
GRN,
outputFolder = NULL,
basenameOutput = NULL,
plotAsPDF = TRUE,
pdf_width = 12,
pdf_height = 12,
title = NULL,
maxEdgesToPlot = 500,
## Here we see the nCommunitiesMax argument
nCommunitiesMax = 8,
graph = "TF-gene",
colorby = "type",
layout = "fr",
vertice_color_TFs = list(h = 10, c = 85, l = c(25, 95)),
vertice_color_peaks = list(h = 135, c = 45, l = c(35, 95)),
vertice_color_genes = list(h = 260, c = 80, l = c(30, 90)),
vertexLabel_cex = 0.4,
vertexLabel_dist = 0,
forceRerun = FALSE
)
## package version - no nCommunitiesMax argument

visualizeGRN(
  GRN,
  outputFolder = NULL,
  basenameOutput = NULL,
  plotAsPDF = TRUE,
  pdf_width = 12,
  pdf_height = 12,
  title = NULL,
  maxRowsToPlot = 500,
  graph = "TF-gene",
  colorby = "type",
  layered = FALSE,
  vertice_color_TFs = list(h = 10, c = 85, l = c(25, 95)),
  vertice_color_peaks = list(h = 135, c = 45, l = c(35, 95)),
  vertice_color_genes = list(h = 260, c = 80, l = c(30, 90)),
  vertexLabel_cex = 0.4,
  vertexLabel_dist = 0,
  forceRerun = FALSE
)