Chapter 12 Pseudobulk Expression

library(Seurat)
library(tidyverse)
library(magrittr)

12.1 Load seurat object

combined <- readRDS('data/Demo_CombinedSeurat_SCT_Preprocess_FilterLQCells.rds')

12.2 Given genes, calculate pseudobulk expression

Idents(combined) <- 'cluster'
DefaultAssay(combined) <- 'RNA'
combined <- NormalizeData(combined)


plotBulkHeatmap <- function(x){
  combined.tmp <- ScaleData(combined, features = x)
  x <- intersect(x, GetAssayData(combined.tmp, slot = 'scale.data'))
  mat <- AverageExpression(combined.tmp, features = x, slot = 'scale.data')
  mat1 <- mat$RNA
  re <- pheatmap::pheatmap(mat1, angle_col = 45,  border = NA)
  return(re)
}


plotBulkHeatmap2 <- function(x){
  x <- intersect(x, rownames(GetAssayData(combined, slot = 'data')))
  mat <- AverageExpression(combined, features = x, slot = 'data')
  mat1 <- t(scale(t(mat$RNA)))
  re <- pheatmap::pheatmap(mat1, angle_col = 45, border = NA)
  return(re)
}

gn <- c('SOX9', 'HOXP', 'MKI67', 'EOMES', 'NEUROD2', 'SATB2', 'NR4A2', 'GAD1', 'GAD2')
plotBulkHeatmap(gn)

## Centering and scaling data matrix

## Finished averaging RNA for cluster RG

## Finished averaging RNA for cluster Cycling

## Finished averaging RNA for cluster OPC

## Finished averaging RNA for cluster IP

## Finished averaging RNA for cluster ExN

## Finished averaging RNA for cluster ExM

## Finished averaging RNA for cluster ExU

## Finished averaging RNA for cluster ExDp

## Finished averaging RNA for cluster InMGE

## Finished averaging RNA for cluster InCGE

## Finished averaging RNA for cluster InPSB

## Finished averaging RNA for cluster Mic

## Finished averaging RNA for cluster Per

## Finished averaging RNA for cluster End

## Finished averaging SCT for cluster RG

## Finished averaging SCT for cluster Cycling

## Finished averaging SCT for cluster OPC

## Finished averaging SCT for cluster IP

## Finished averaging SCT for cluster ExN

## Finished averaging SCT for cluster ExM

## Finished averaging SCT for cluster ExU

## Finished averaging SCT for cluster ExDp

## Finished averaging SCT for cluster InMGE

## Finished averaging SCT for cluster InCGE

## Finished averaging SCT for cluster InPSB

## Finished averaging SCT for cluster Mic

## Finished averaging SCT for cluster Per

## Finished averaging SCT for cluster End

plotBulkHeatmap2(gn)

## Finished averaging RNA for cluster RG

## Finished averaging RNA for cluster Cycling

## Finished averaging RNA for cluster OPC

## Finished averaging RNA for cluster IP

## Finished averaging RNA for cluster ExN

## Finished averaging RNA for cluster ExM

## Finished averaging RNA for cluster ExU

## Finished averaging RNA for cluster ExDp

## Finished averaging RNA for cluster InMGE

## Finished averaging RNA for cluster InCGE

## Finished averaging RNA for cluster InPSB

## Finished averaging RNA for cluster Mic

## Finished averaging RNA for cluster Per

## Finished averaging RNA for cluster End

## Finished averaging SCT for cluster RG

## Finished averaging SCT for cluster Cycling

## Finished averaging SCT for cluster OPC

## Finished averaging SCT for cluster IP

## Finished averaging SCT for cluster ExN

## Finished averaging SCT for cluster ExM

## Finished averaging SCT for cluster ExU

## Finished averaging SCT for cluster ExDp

## Finished averaging SCT for cluster InMGE

## Finished averaging SCT for cluster InCGE

## Finished averaging SCT for cluster InPSB

## Finished averaging SCT for cluster Mic

## Finished averaging SCT for cluster Per

## Finished averaging SCT for cluster End