Different evaluation test on harmony integration on patient origin and cell_line-theta-0.5 both

1. load libraries

2. Load Seurat Object

#Load Seurat Object merged from cell lines and a control after filtration
load("../0-R_Objects/CD4Tcells_harmony_integrated_0.5_theta_patientorigin_cell_line.Robj")

3. Harmony Visualization

DimPlot(All_samples_Merged, 
              reduction = "umap", 
              group.by = "cell_line",
              label = TRUE, 
              label.box = TRUE) 

    

DimPlot(All_samples_Merged, 
              reduction = "umap", 
              group.by = "harmony_res_0.1",
              label = TRUE, 
              label.box = TRUE) 

DimPlot(All_samples_Merged, 
              reduction = "umap", 
              group.by = "harmony_res_0.2",
              label = TRUE, 
              label.box = TRUE) 

DimPlot(All_samples_Merged, 
              reduction = "umap", 
              group.by = "harmony_res_0.3",
              label = TRUE, 
              label.box = TRUE) 

DimPlot(All_samples_Merged, 
              reduction = "umap", 
              group.by = "harmony_res_0.4",
              label = TRUE, 
              label.box = TRUE) 

DimPlot(All_samples_Merged, 
              reduction = "umap", 
              group.by = "harmony_res_0.5",
              label = TRUE, 
              label.box = TRUE) 

DimPlot(All_samples_Merged, 
              reduction = "umap", 
              group.by = "harmony_res_0.6",
              label = TRUE, 
              label.box = TRUE) 

DimPlot(All_samples_Merged, 
              reduction = "umap", 
              group.by = "harmony_res_0.7",
              label = TRUE, 
              label.box = TRUE) 

DimPlot(All_samples_Merged, 
              reduction = "umap", 
              group.by = "harmony_res_0.8",
              label = TRUE, 
              label.box = TRUE) 

DimPlot(All_samples_Merged, 
              reduction = "umap", 
              group.by = "harmony_res_0.9",
              label = TRUE, 
              label.box = TRUE) 

DimPlot(All_samples_Merged, 
              reduction = "umap", 
              group.by = "harmony_res_1",
              label = TRUE, 
              label.box = TRUE) 

DimPlot(All_samples_Merged, 
              reduction = "umap", 
              group.by = "harmony_res_1.2",
              label = TRUE, 
              label.box = TRUE) 

DimPlot(All_samples_Merged, 
              reduction = "umap", 
              group.by = "predicted.celltype.l1",
              label = TRUE, 
              label.box = TRUE) 

DimPlot(All_samples_Merged, 
              reduction = "umap", 
              group.by = "predicted.celltype.l2",
              label = TRUE, 
              label.box = TRUE) 

DimPlot(All_samples_Merged, 
              reduction = "umap", 
              group.by = "predicted.celltype.l3",
              label = TRUE, 
              label.box = TRUE)