CCCheatmap

The goal of CCCheatmap is to build custom heatmaps from the output of CellChat. These are modified versions of the heatmaps produced by their command \code{netVisual_heatmap}. It allows the user to choose specific populations as senders and receivers for which to consider signaling. The colors are the sum of the communication probabilities for a given pathway between two designated cell types.

Installation

You can install the development version of CCCheatmap from GitHub with:

# install.packages("devtools")
devtools::install_github("lkroeh/CCCheatmap")

Example

This is a basic example which shows you how to make a heatmap:

library(CCCheatmap)
cellchatobject
hm <- makehm(cellchatobject)
hm

#example color mapping
col_fun = colorRamp2(c(0, 0.0001, 0.01, 0.035, 2.5), c("grey", "lightyellow", "lightblue1","lightblue2", "blue"))
#The function will also output the quantiles of the data used in the heatmap, which will help you map the colors

#Detailed Example
makehm(cellchat,
       col_fun = colorRamp2(c(0, 0.0001, 0.01, 0.035, 2.5), c("grey", "lightyellow", "lightblue1","lightblue2", "blue")),
       sources = c("Epi1", "Epi2", "Epi3", "Epi4", "Epi5", "Epi6", "Epi7"),
       targets = levels(cellchat@idents),
       fontsize = 10,
       hmtitle = "outgoing Epi signaling")