Description
Hi,
I am using pycisTopic. My multiome data was processed in seurat/signac. I added seurat_clusters seurat/signac as metadata column.
cell_data = pd.read_csv(projDir+'metadata.txt', sep='\t')
cell_data.set_index('cell', inplace=True)
cistopic_obj.add_cell_data(cell_data)
Then I also added UMAP coordinates from seurat/signac
umap_coordinates = pd.read_csv("umap_coordinates.tsv", sep="\t")
umap_coordinates.set_index('cell', inplace=True)
cistopic_obj.projections["cell"]["umap"] = umap_coordinates
umap_coordinates.index = cistopic_obj.cell_data.index
Now when plotting the metadata, it is giving umap with seurat_cluster as continuous data, continuous scale color.......... not individual color for each cluster:
plot_metadata(cistopic_obj,
reduction_name='umap',
variables=['seurat_clusters'],
target='cell',
show_legend=1,
show_label=1,
num_columns=2,
text_size=10,
dot_size=5,
figsize=(15,5),
save= outDir + 'visualization/dimensionality_reduction_label.pdf')
However, if I run "find_clusters" then I get leiden cluster image with discrete colors. How can I visualize my seurat clusters in seurat umap? Well, a quick hack is to add a letter like "C" before the cluster number though.
thanks,