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Run CellChat analysis

Source: R/RunCellChat.R
RunCellChat.Rd

Run CellChat analysis

Usage

RunCellChat(
  srt,
  group.by,
  species = c("Homo_sapiens", "Mus_musculus", "zebrafish"),
  split.by = NULL,
  annotation_selected = NULL,
  group_column = NULL,
  group_cmp = NULL,
  thresh = 0.05,
  min.cells = 10,
  do.fast = FALSE,
  backend = c("cpp", "r"),
  assay = NULL,
  layer = "data",
  verbose = TRUE
)

Arguments

srt

A Seurat object.

group.by

Metadata column(s) used to color cells.

species

"Homo_sapiens", "Mus_musculus", or "zebrafish".

split.by

Metadata column to facet by.

annotation_selected

Cell types to include. NULL uses all.

group_column

Metadata column defining conditions or groups.

group_cmp

Pairwise condition comparisons for differential CellChat.

thresh

Threshold for centrality scores.

min.cells

Minimum expressed cells required for genes used in CCC.

do.fast

Use CellChat's fast Wilcoxon via presto (must be installed).

backend

Post-processing / unified CCC table backend. Does not change upstream CellChat inference.

assay

Assay to use. NULL uses the default assay.

layer

Assay layer to use.

verbose

Whether to print the message. Default is TRUE.

Value

A Seurat object with CellChat results stored in srt@tools[["CellChat"]].

References

CellChat

See also

CCCHeatmap, CCCStatPlot, CCCNetworkPlot

Examples

data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
#> ℹ [2026-08-30 04:50:26] Start standard processing workflow...
#> ℹ [2026-08-30 04:50:26] Checking a list of <Seurat>...
#> ! [2026-08-30 04:50:26] Data 1/1 of the `srt_list` is "unknown"
#> Warning: Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-08-30 04:50:26] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 04:50:26] Perform `FindVariableFeatures()` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 04:50:27] Use the separate HVF from `srt_list`
#> ℹ [2026-08-30 04:50:27] Number of available HVF: 2000
#> ℹ [2026-08-30 04:50:27] Finished check
#> ℹ [2026-08-30 04:50:27] Perform `ScaleData()`
#> ℹ [2026-08-30 04:50:27] Perform pca linear dimension reduction
#> ℹ [2026-08-30 04:50:27] Use stored estimated dimensions 1:23 for Standardpca
#> ℹ [2026-08-30 04:50:28] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-08-30 04:50:28] Reorder clusters...
#> ℹ [2026-08-30 04:50:28] Skip `log1p()` because `layer = data` is not "counts"
#> ℹ [2026-08-30 04:50:28] Perform umap nonlinear dimension reduction
#> ✔ [2026-08-30 04:50:35] Standard processing workflow completed
pancreas_sub <- RunCellChat(
  pancreas_sub,
  group.by = "CellType",
  species = "Mus_musculus"
)
#> ℹ [2026-08-30 04:50:35] Start CellChat analysis
#> [1] "Create a CellChat object from a data matrix"
#> Set cell identities for the new CellChat object 
#> The cell groups used for CellChat analysis are  Ductal, Endocrine, Ngn3-high-EP, Ngn3-low-EP, Pre-endocrine 
#> ! [2026-08-30 04:50:35] Function "CellChatDB.mouse" not found in CellChat namespace
#> Warning: Function "CellChatDB.mouse" not found in CellChat namespace
#> The number of highly variable ligand-receptor pairs used for signaling inference is 841 
#> triMean is used for calculating the average gene expression per cell group. 
#> [1] ">>> Run CellChat on sc/snRNA-seq data <<< [2026-08-30 04:50:37.726818]"
#> [1] ">>> CellChat inference is done. Parameter values are stored in `object@options$parameter` <<< [2026-08-30 04:50:55.332709]"
#> ✔ [2026-08-30 04:50:55] CellChat analysis completed

CCCNetworkPlot(
  pancreas_sub,
  method = "CellChat",
  plot_type = "bipartite"
)


CCCHeatmap(
  pancreas_sub,
  method = "CellChat",
  plot_type = "heatmap"
)


CCCStatPlot(
  pancreas_sub,
  method = "CellChat",
  plot_type = "violin",
  top_n = 50
)