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jinworks / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
GNU General Public License v3.0
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#error regarding cellchat object #77

Open surinderchd opened 9 months ago

surinderchd commented 9 months ago

Dear Sir/Madam,

i am having this error while working with cellchat, please guide mr to solve this error,

cellchatnew <- createCellChat(object = PTstroma_traj, group.by = "Group", assay = "RNA") [1] "Create a CellChat object from a Seurat object" The meta.data slot in the Seurat object is used as cell meta information The cell barcodes in 'meta' is AAACGCTCATGCCGAC-1_1 AACCAACCAACTAGAA-1_1 AACCTGACAAATCCCA-1_1 AACGTCATCTTTGCAT-1_1 AACTTCTTCCCGAGGT-1_1 AACTTCTTCGCGAAGA-1_1 Error in .rowNamesDF<-(x, value = value) : invalid 'row.names' length In addition: Warning messages: 1: In LayerData.Assay5(object = x, layer = i) : multiple layers are identified by data.BDP3_db/m.1 data.1 data.BDP4_db/db.2 data.2 data.BDP5_SGLT2i.3 data.3 data.BDP6_SGLT2i-aPC.4 data.4 data.BDP7_db/m.5 data.5 data.BDP8_db/db.6 data.6 data.BDP9_SGLT2i.7 data.7 data.BDP10_SGLT2i-aPC.8 data.8 only the first layer is used 2: In createCellChat(object = PTstroma_traj, group.by = "Group", assay = "RNA") : The cell barcodes in 'meta' is different from those in the used data matrix. We now simply assign the colnames in the data matrix to the rownames of 'mata'!

sqjin commented 9 months ago

@surinderchd It looks like you are working on a Seurat v5 object. It should work if you re-install the package.

surinderchd commented 9 months ago

Dear Sir @sqjin , Thank you for your reply, do i need to reinstall seurat or cellchat?