Integration by Harmony_on_SCTransform_DATA

1. load libraries

2. Load Seurat Object

  All_samples_Merged

An object of class Seurat 
62625 features across 46976 samples within 6 assays 
Active assay: SCT (25901 features, 3000 variable features)
 3 layers present: counts, data, scale.data
 5 other assays present: RNA, ADT, prediction.score.celltype.l1, prediction.score.celltype.l2, prediction.score.celltype.l3
 4 dimensional reductions calculated: pca, umap, integrated_dr, ref.umap

3. Data PREPERATION

ElbowPlot(All_samples_Merged)

# plot
before <- DimPlot(All_samples_Merged, reduction = "umap", group.by = "cell_line", label = TRUE, label.box = TRUE, repel = TRUE)



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

NA
NA
NA

4. Harmony-integration

after <- DimPlot(All_samples_Merged_Harmony_Integrated, reduction = "umap", group.by = "cell_line", label = TRUE, label.box = TRUE, repel = TRUE)

before|after

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



DimPlot(All_samples_Merged_Harmony_Integrated,reduction = "umap", group.by = "SCT_snn_res.0.5", label = TRUE, label.box = TRUE, repel = TRUE)

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

FeaturePlot

myfeatures <- c("CD3E", "CD4", "CD8A", "NKG7", "GNLY", "MS4A1", "CD14", "LYZ", "MS4A7", "FCGR3A", "CST3", "FCER1A")

FeaturePlot(All_samples_Merged_Harmony_Integrated, reduction = "umap", dims = 1:2, features = myfeatures, ncol = 4, order = T) + NoLegend() + NoAxes() + NoGrid()

Warning: All cells have the same value (0) of "FCER1A"

5. Save the Seurat object as an Robj file

# save(All_samples_Merged_Harmony_Integrated, file = "All_samples_Merged_Harmony_Integrated.Robj")