Chapter 24 Annotate by Gene Scores for Canonical Genes

library(ArchR)
set.seed(1)

24.1 Description

• Visualize gene scores for canonical marker genes to annotate

24.2 Set env and load arrow project

## Section: set default para
##################################################
addArchRThreads(threads = 16) # setting default number of parallel threads


## Section: load object
##################################################
proj <- loadArchRProject(path = "data/ArchR/ArrowProject/Merged/")


## Section: imputation
##################################################
proj <- addImputeWeights(proj, reducedDims = "IterativeLSI_peak")

24.3 Visualize gene scores

markerGenes <- c("HES1", "PAX6", 
                 "PPP1R17", "EOMES", 
                 "NEUROD6", "STMN2", 
                 "GAD1", "GAD2")

p <- plotEmbedding(
  ArchRProj = proj,
  colorBy = "GeneScoreMatrix",
  name = markerGenes,
  embedding = "UMAP_peak",
  quantCut = c(0.01, 0.95),
  size = 0.5,
  imputeWeights = getImputeWeights(proj)
)

## Getting ImputeWeights

## ArchR logging to : ArchRLogs/ArchR-plotEmbedding-259e7cb04bd7-Date-2021-11-12_Time-14-58-55.log
## If there is an issue, please report to github with logFile!

## Getting UMAP Embedding

## ColorBy = GeneScoreMatrix

## Getting Matrix Values...

## 2021-11-12 14:58:58 :

## 

## Imputing Matrix

## Using weights on disk

## 1 of 1

## Plotting Embedding

## 1 2 3 4 5 6 7 8 
## ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-259e7cb04bd7-Date-2021-11-12_Time-14-58-55.log

#Rearrange for grid plotting
p2 <- lapply(p, function(x) {
  x + guides(color = FALSE, fill = FALSE) +
    theme_ArchR(baseSize = 6.5) +
    theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
    theme(
      axis.text.x = element_blank(),
      axis.ticks.x = element_blank(),
      axis.text.y = element_blank(),
      axis.ticks.y = element_blank()
    )
})

do.call(cowplot::plot_grid, c(list(ncol = 2),p2))