BlishLab / scriabin

Analysis of cell-cell communication at single-cell resolution
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Common errors when running BinDatasets #11

Closed ZZZhuLF closed 1 year ago

ZZZhuLF commented 1 year ago

Just like another unresolved issue, I have also encountered this problem, whether using the example data or my own data. Comments regarding this issue have been ongoing from 2022 until recently, and everyone has faced the exact same problem. Please forgive me for submitting another issue to gain the attention of the author's team. This is because I am really eager to use Scriabin in my own research!

ifnb <- BinDatasets(ifnb, split.by = "stim", dims = 1:30,coarse_cell_types = "coarse_ident", sigtest_cell_types = "seurat_annotations")

Setting optim_k.unique to 1.33 Binning with coarse cell types Constructing neighbor graphs with reduction pca . . . Splitting object . . . Preparing integration . . . Generating anchorsets . . . Computing 2000 integration features Scaling features for provided objects Finding all pairwise anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 16193 anchors Filtering anchors Retained 5133 anchors Mapping anchor names . . . Generating anchor bins . . . Generating connectivity matrix . . . Optimizing number of bins . . . Error in if (check_completion(nbs_completion)) { : the condition has length > 1

ajwilk commented 1 year ago

Hi there, responding in #7