Resolution-0.3-to-2-Notebook

1. load libraries

2. Load Seurat Object

#Load Seurat Object merged from cell lines and a control(PBMC) after filtration
SS_All_samples_Merged <- load("Different_Resolution_on_my_UMAP-0.3-to-2.Robj")

All_samples_Merged

An object of class Seurat 
63098 features across 49193 samples within 3 assays 
Active assay: SCT (26469 features, 3000 variable features)
 3 layers present: counts, data, scale.data
 2 other assays present: RNA, ADT
 2 dimensional reductions calculated: pca, umap

3. Visualization

UMAPPlot(All_samples_Merged,group.by = "cell_line", 
        reduction = "umap",
        label.size = 3,
        repel = T,
        label = T)

UMAPPlot(All_samples_Merged,
        group.by = "SCT_snn_res.0.3", 
        reduction = "umap",
        label.size = 3,
        repel = T,
        label = T)

UMAPPlot(All_samples_Merged,
        group.by = "SCT_snn_res.0.5", 
        reduction = "umap",
        label.size = 3,
        repel = T,
        label = T)

UMAPPlot(All_samples_Merged,
        group.by = "SCT_snn_res.0.7", 
        reduction = "umap",
        label.size = 3,
        repel = T,
        label = T)

UMAPPlot(All_samples_Merged,
        group.by = "SCT_snn_res.1", 
        reduction = "umap",
        label.size = 3,
        repel = T,
        label = T)

UMAPPlot(All_samples_Merged,
        group.by = "SCT_snn_res.1.2", 
        reduction = "umap",
        label.size = 3,
        repel = T,
        label = T)

UMAPPlot(All_samples_Merged,
        group.by = "SCT_snn_res.1.5", 
        reduction = "umap",
        label.size = 3,
        repel = T,
        label = T)

UMAPPlot(All_samples_Merged,
        group.by = "SCT_snn_res.1.7", 
        reduction = "umap",
        label.size = 3,
        repel = T,
        label = T)

UMAPPlot(All_samples_Merged,
        group.by = "SCT_snn_res.2", 
        reduction = "umap",
        label.size = 3,
        repel = T,
        label = T)