Cell-cell communication network plot — plot_communication

This function is used to plot the results of the cell-cell communication analysis overlapped to the single-cell plot

Usage

plot_communication_network(
  cell_emb,
  cl_res,
  cl_cell,
  palette,
  e_scale = 9,
  label,
  save_file,
  point_size = 0.5,
  point_alpha = 0.5,
  edge_alpha = 0.8,
  edge_color = "gray45",
  node_size = 5,
  text_size = 2,
  text_color = "black",
  heigh = 100,
  width = 100,
  res = 300,
  unit = "mm"
)

Arguments

cell_emb: cell embedding (UMAP or tSNE) matrix
cl_res: cell-cell communication results (from `gs_cross_talk()`)
cl_cell: two column data-frame, the first should be the cell names, the second the annotation (cluster or cell types)
palette: named vector of the color associated to each cluster or cell types, and it will be used to set both cell points and communication network vertices color. If NULL ignored, ggplot automatic palette used
e_scale: value to scale the edge weights for plotting, change to adjust maximum link widths
label: logical, if cluster/cell type name should be plotted on the vertex names
save_file: saving plot name. If NULL ignored
point_size: = 0.5 size of the cell points to be plotted.
point_alpha: = 0.5 transparency of the color fill of the cell points
edge_alpha: = 0.8 transparency of the edge color
edge_color: = edge color
node_size: = 5 size of the vertices of the cell-cell communication network overlapped to the cell points
text_size: size of the node labels plotted (if `label = T`)
text_color: = text color (if `label = T`)
heigh, width, res, unit: params used to save plot (in jpeg format)

Details

This functions uses the cell-embeddings produced by the single-cell analysis and the cell-cell communication analysis results, obtained with `gs_cross_talk()`, to plot the communication network overlapped to the cell plot. This functions do not filter the `gs_cross_talk()` results to plot only the significant ones. Cells and communication network vertices are colored according to the annotation, provided with `cl_cell`