Hello,
I've been following the Joint RNA and ATAC analysis: 10x multiomic tutorial with my own snRNAseq + snATACseq data. I've completed all steps until the Joint UMAP visualization step. I skipped the annotating cell types step because I don't have annotations for this data yet, which is from the Primary Visual Cortex (V1) from Macaca fascicularis. I'm trying to create a UMAP for my 7 samples, but I'm not sure why it isn't generating a normal UMAP with cluster id's for each cluster. Below is my code for sample 1.
# build a joint neighbor graph using both assays
liftoff_1_MI5_V1_SO <- FindMultiModalNeighbors(
object = liftoff_1_MI5_V1_SO,
reduction.list = list("pca", "lsi"),
dims.list = list(1:50, 2:40),
modality.weight.name = "RNA.weight",
verbose = TRUE
)
# build a joint UMAP visualization
liftoff_1_MI5_V1_SO <- RunUMAP(
object = liftoff_1_MI5_V1_SO,
nn.name = "weighted.nn",
assay = "RNA",
verbose = TRUE
)
DimPlot(liftoff_1_MI5_V1_SO, label = TRUE, repel = TRUE, reduction = "umap") + NoLegend()
# not sure why everything is one color?
It seems to color all the cells by orig.ident
which is not what I was expecting. I then tried the standard Seurat steps from their Guided Clustering Tutorial to generate the UMAP, but I was getting errors.
liftoff_1_MI5_V1_SO <- FindNeighbors(liftoff_1_MI5_V1_SO, dims = 1:30, return.neighbor = TRUE)
# Computing nearest neighbor graph
# Computing SNN
liftoff_1_MI5_V1_SO <- FindClusters(liftoff_1_MI5_V1_SO, resolution = c(0.4, 0.5, 0.6, 0.7, 0.8))
# Error in FindClusters.Seurat(liftoff_1_MI5_V1_SO, resolution = c(0.4, :
# Provided graph.name not present in Seurat object
liftoff_1_MI5_V1_SO <- RunUMAP(liftoff_1_MI5_V1_SO, dims = 1:30)
DimPlot(liftoff_1_MI5_V1_SO, reduction = "umap", label = TRUE)
I'm not sure why I'm getting this error? Do I need to run the Seurat steps to generate the UMAP for each sample? Do I need to run the standard Seurat Find Neighbors, Find Clusters, RunUMAP, & DimPlot separately for the RNA assay and the ATAC assay before making a joint UMAP? How can I calculate the resolution for the joint (snRNAseq + snATACseq) UMAP? How can I make the UMAP so that each cluster has a cluster ID and each cluster has a different color like normal?
Thanks for your response. I was able to fix this by first making the UMAP for the snRNAseq assay. I re-ran FindNeighbors and then re-ran FindClusters after specifying the neighbor method to use to find clusters with the graph.name parameter.
Next, I made a separate UMAP for the snATACseq assay.
Lastly, I made a combined multiomics UMAP (snRNAseq + snATACseq) using the following tutorial.