Could not find any LRpairs on stereo-seq data

[cynthier]

Hi, thanks for your tools!

Since the stereo-seq data is single-cell level, I follow the tutorial of single-cell ST data, using the custom LRs and pathway in the "Data". But after the "find_lr_path", there is no LR pairs in the object and the following steps could not be continued. There is more than five cell types in my data. Did I miss something?

obj <- SpaTalk::createSpaTalk(st_data, st_meta,species="Mouse", if_st_is_sc = T, spot_max_cell = 1, celltype = as.character(st$region))

obj

An object of class SpaTalk
15488 genes across 3654 single-cells (0 lrpair)

load("../Spatalk/Code_github/data/lrpairs.rda") load("../Spatalk/Code_github/data/pathways.rda")
obj <- find_lr_path(object = obj, lrpairs = lrpairs, pathways = pathways,use_n_cores = 10)
Checking input data
Begin to filter lrpairs and pathways
Done

obj
An object of class SpaTalk
15488 genes across 3654 single-cells (0 lrpair)

obj <- dec_cci_all(obj, min_pairs = 1, use_n_cores = 10, per_num = 100, n_neighbor = 50)
Note: there are 8 cell types and 56 pair-wise cell pairs
Begin to find LR pairs
Error in { : task 1 failed - "invalid character indexing"