harmonizing2.Rmd

---
title: "Data_wrangling"
author: "Ralf"
date: "October 15, 2020"
output: html_document
---




```{r Aortic stenosis data}
library(tictoc)
data_hca$dataset <- factor(rep("hca",ncol(data_hca)))
combined_filtered$dataset <- factor(rep("aort_sten",ncol(combined_filtered)))
combined_filtered$region <- factor(rep("SP",ncol(combined_filtered)))

human_heart <- merge(data_hca,combined_filtered,c("hca","aort_sten"))

seurat_object <- NormalizeData(human_heart) %>%
FindVariableFeatures(selection.method = "vst", nfeatures = 2000) %>%
ScaleData() %>%
RunPCA()

#ElbowPlot(seurat_object, ndims = 50)
#tic()
#seurat_object <- RunUMAP(seurat_object, reduction = "pca", dims = 1:15,reduction.name = "umap_before") %>% 
#    FindNeighbors(reduction = "pca", dims = 1:15) %>% 
#    FindClusters(resolution = 0.5)
#toc()

#p2 <- DimPlot(seurat_object, reduction = "umap_before", pt.size = .1, group.by = "dataset")
#p2$layers[[1]]$aes_params$alpha <- 0.1
#p2$data$dataset <- factor(p2$data$dataset, levels = c("hca","aort_sten"))
#ggsave("/media/Helios_scStorage/Ralf/Heart_cell_atlas/data/output/umap_aorta_sten_before_harmony.png", p2, device = "png")

tic()
seurat_object <- RunHarmony(seurat_object, "dataset", plot_convergence = T)
toc()
#1st: 1253.965 sec elapsed
# 1233.707 sec elapsed

# After Harmony integration
#ElbowPlot(seurat_object, ndims = 50)
tic()
seurat_object <- RunUMAP(seurat_object, reduction = "harmony", dims = 1:15) %>% 
    FindNeighbors(reduction = "harmony", dims = 1:15) %>% 
    FindClusters(resolution = 0.5)
toc()

## Save and write seurat object and create plots for meeting
rm(data_hca)
rm(human_heart)
plots_out_path <- "/media/Helios_scStorage/SingleCell/Human/WholeHeart/Heart_cell_atlas_aortic_stenosis_harmonized/Harmonized_whole_dataset_only_as_only_septum_only_nuc/plots/"

seurat_object_diet <- DietSeurat(seurat_object, dimreducs = c("pca","harmony", "umap"),graphs = c("RNA_nn","RNA_snn"))
saveRDS(seurat_object_diet,"/media/Helios_scStorage/SingleCell/Human/WholeHeart/Heart_cell_atlas_aortic_stenosis_harmonized/Harmonized_whole_dataset_only_as_only_septum_only_nuc/seurat_object_hca_as_harmonized_AS_SP_nuc.rds")
```