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())