Using a contribution score of each cell group to each signaling pathway computed by multiplying W by H obtained from `identifyCommunicationPatterns`, we constructed a dot plot in which the dot size is proportion to the contribution score to show association between cell group and their enriched signaling pathways.
netAnalysis_dot(
object,
slot.name = "netP",
pattern = c("outgoing", "incoming"),
cutoff = NULL,
color.use = NULL,
pathway.show = NULL,
group.show = NULL,
shape = 21,
dot.size = c(1, 3),
dot.alpha = 1,
main.title = NULL,
font.size = 10,
font.size.title = 12
)CellChat object
the slot name of object that is used to compute centrality measures of signaling networks
"outgoing" or "incoming"
the threshold for filtering out weak links. Default is 1/R where R is the number of latent patterns. We set the elements in W and H to be zero if they are less than `cutoff`.
the character vector defining the color of each cell group
the character vector defining the signaling to show
the character vector defining the cell group to show
the shape of the symbol: 21 for circle and 22 for square
a range defining the size of the symbol
transparency
the title of plot
font size of the text
font size of the title