Command log overwritten for RunTSNE and FindClusters

[kverstae]

Hi,

We would like to use the commands slot of the Seurat object to keep track of all the parameters used for the different steps during the analysis. Since we have multi-modal data (cDNA + antibody data), we run (parts of) the Seurat pipeline for both modalities. One of these steps is FindClusters, which we use to both cluster the data on the gene expression data and the antibody data separately. On the second run of FindClusters, the first entry in the command log is overwritten:

FindClusters(seuratObj, graph.name = "RNA_snn", resolution = 0.6)
FindClusters(seuratObj, graph.name = "ADT_snn", resolution = 0.8)
names(seuratObj@commands) # Only includes FindClusters once with the parameters of the last run

Would it be possible to add the graph.name parameter in the command log so we can keep track of all the different FindCluster runs?

A similar story for RunTSNE. This also overwrites and only keeps the results of the last run. I expect this to behave the same as RunUMAP which creates command logs with following key format: RunUMAP.<ASSAY>.<REDUCTION>