Visualizes CellChat analysis results with various plot types including circle plots, heatmaps, bubble plots, and spatial signaling plots.
Usage
Plot_NicheCellComm(
STID_obj = NULL,
samp_mode = "SS",
loop_id = "LoopAllSamp",
CellComm_data = NULL,
sources.use = NULL,
targets.use = NULL,
signaling = NULL,
pairLR.use = NULL,
col = NULL
)Arguments
- STID_obj
An STID object containing niche analysis results
- samp_mode
Character, sample type - "SS" or "MS" (default: "SS")
- loop_id
Character, sample grouping identifier (default: "LoopAllSamp")
- CellComm_data
List, CellChat results from CalSampCellComm
- sources.use
Character vector, source cell types to include
- targets.use
Character vector, target cell types to include
- signaling
Character vector, signaling pathways to plot
- pairLR.use
Data frame, specific ligand-receptor pairs to plot
- col
Named vector, colors for cell types
Examples
if (FALSE) { # \dontrun{
# Plot CellChat results
Plot_NicheCellComm(
STID_obj = STID_obj,
CellComm_data = cellcomm_results,
signaling = c("TGFb", "WNT"),
sources.use = "Epithelial",
targets.use = "Immune"
)
} # }