def cluster_markers(rdata, tenx_analysis, rep, pcs, embedding_file, prefix):
tenx = TenxAnalysis(tenx_analysis)
tenx.load()
sce = SingleCellExperiment.fromRData(rdata)
markers = tenx.markers_by_clusters(sce, rep="PCA", pcs=pcs)
markers_by_cluster = list(zip(*markers["rank_genes_groups"]["names"]))
for i, markers in enumerate(markers_by_cluster):
cluster_prefix = "Cluster {} {}".format(i, prefix)
plot_by_markers(rdata, tenx_analysis, markers, cluster_prefix, rep,
pcs, embedding_file)
def scvis_by_cluster_markers(rdata, tenx_analysis, prefix, pcs,
embedding_file):
try:
tenx = TenxAnalysis(tenx_analysis)
tenx.load()
sce = SingleCellExperiment.fromRData(rdata)
cluster_labels = tenx.markers_by_clusters(
sce, rep="SCVIS", pcs=pcs, embedding_file=embedding_file)
except Exception as e:
return
def umap_by_cluster_markers(rdata, tenx_analysis, prefix, pcs):
tenx = TenxAnalysis(tenx_analysis)
tenx.load()
sce = SingleCellExperiment.fromRData(rdata)
markers = tenx.markers_by_clusters(sce, rep="UMAP", pcs=pcs)
print(markers.keys())
