cellchat analysis from from a Scanpy h5ad file

Question

[cgp09741]

I am currently trying to generate a cellchat analysis created from a Scanpy h5ad file but I am encountering an error when it comes to the computeCommunProb below is the code that i am running along with the error. If anyone has insight as to where I am going wrong in the transfer of my h5ad file to a cellchat onject it would be greatly appreciated.

ad <- import("anndata", convert = FALSE)

ad_object <- ad$read_h5ad("/adata.h5ad")

# access normalized data matrix
data.input <- t(py_to_r(ad_object$X))

rownames(data.input) <- rownames(py_to_r(ad_object$var))

colnames(data.input) <- rownames(py_to_r(ad_object$obs))

# access meta data
meta.data <- py_to_r(ad_object$obs)
colnames(meta.data) <- c("doublet_scores", "predicted_doublets", "mito_fraction", "n_counts", "n_genes", "total_counts", "sample", "batch", "leiden", "cell_type")
meta.data <- select(meta.data, cell_type)
meta.data <- meta.data %>% rename(group = cell_type)

meta <- meta.data

cellchat <- createCellChat(object = data.input, meta = meta, group.by = "group")
cellchat <- addMeta(cellchat, meta = meta, meta.name = "group")
cellchat <- setIdent(cellchat, ident.use = "group")
levels(cellchat@idents)


CellChatDB.human <- CellChatDB.human # Load the human database 
showDatabaseCategory(CellChatDB.human)
# Set all CellChatDB for cell-cell communication analysis
CellChatDB.use <- CellChatDB.human
cellchat@DB <- CellChatDB.use

cellchat <- subsetData(cellchat)

# Pre-processing the expression data
cellchat <- identifyOverExpressedGenes(cellchat)
cellchat <- identifyOverExpressedInteractions(cellchat)

# Optional: project gene expression data onto protein-protein interaction (PPI)
cellchat <- projectData(cellchat, PPI.human)

# 4. Compute the communication probability and infer cellular communication network
cellchat <- computeCommunProb(cellchat)
cellchat <- computeCommunProb(cellchat, raw.use = FALSE) # use the projected data

0%Error in if (sum(P1_Pspatial) == 0) { : missing value where TRUE/FALSE needed