cell types are not in same order from left to right in both datasets when comparing two group of samples

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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cell types are not in same order from left to right in both datasets when comparing two group of samples #139

Closed tumorscholar closed 3 weeks ago

tumorscholar commented 4 months ago

I am comparing two groups of samples using Comparison analysis of multiple datasets using CellChat vignette. While using the "(B) Compare outgoing (or incoming) signaling patterns associated with each cell population" function I am getting

Could you please help What could be the reason the order of cell types from left to right is not matching in X axis? This is further messing up with downstream analysis.

Thank you

TdzBAS commented 4 months ago

I am facing the same issue.

TdzBAS commented 3 months ago

@sqjin do you have a fix for this?

tumorscholar commented 3 weeks ago

I managed to solve this by

using the same no of clusters in both objects and,
sorting/arranging the cluster/celltype in same order in the Seurat object before subjecting them to CellChat