Changes between Version 58 and Version 59 of SOP/scRNA-seq

Timestamp:

04/25/24 11:27:04 (3 weeks ago)

Author:

gbell

Comment:

--

SOP/scRNA-seq

@@ -207 +207 @@
 }}}
 The clustering at different resolutions are stored in all_Filt$RNA_snn_res.0.3, all_Filt$RNA_snn_res.0.4, and all_Filt$RNA_snn_res.0.5
+
+=== Optimize UMAP plots === 
+
+Default UMAP plots have at least two shortcomings: (1) axes are labeled like 'UMAP_1' instead of the clearer-to-read 'UMAP 1', and (2) cluster numbering starts with 0, even though most people start counting at 1.  These can both be corrected.
+
+{{{
+# Change the x-axis and y-axis labels from "UMAP_1/UMAP_2" to "UMAP 1/UMAP 2"
+DimPlot(all_Filt, reduction = "umap") + xlab('UMAP 1') +  ylab('UMAP 2') + ggtitle('UMAP with relabeled axes') + theme(plot.title = element_text(hjust = 0.5))
+# Rename the cluster numbers by adding 1
+all_Filt$new_labels <- as.numeric(as.character(all_Filt$seurat_clusters)) + 1
+# Plot the cells using these new labels
+DimPlot(all_Filt, reduction = "umap", group.by = "new_labels") + xlab('UMAP 1') +  ylab('UMAP 2') + ggtitle('UMAP with relabeled axes and new cluster numbers') + theme(plot.title = element_text(hjust = 0.5))
+# Add cluster labels (slightly transparent) on top of each cluster
+DimPlot(all_Filt, reduction = "umap", group.by = "new_labels", label = T, label.size=10, label.color="#00000088") + xlab('UMAP 1') +  ylab('UMAP 2') + ggtitle('Final UMAP') + theme(plot.title = element_text(hjust = 0.5))
+}}}
+
 === Identify genes that differentially expressed between samples or clusters === 
 
@@ -234 +250 @@
                                         ident.2 = "18"
 }}}
+
 === Add biological annotations to cells or cell clusters  ===