9.4 Visualizing Marker Genes on an Embedding

As mentioned previously, we can overlay per-cell gene scores on our UMAP embedding. This is accomplished using the colorBy and name parameters in the plotEmbedding() function.

markerGenes  <- c(
    "CD34",  #Early Progenitor
    "GATA1", #Erythroid
    "PAX5", "MS4A1", "MME", #B-Cell Trajectory
    "CD14", "MPO", #Monocytes
    "CD3D", "CD8A"#TCells
  )

p <- plotEmbedding(
    ArchRProj = projHeme2, 
    colorBy = "GeneScoreMatrix", 
    name = markerGenes, 
    embedding = "UMAP",
    quantCut = c(0.01, 0.95),
    imputeWeights = NULL
)
## ArchR logging to : ArchRLogs/ArchR-plotEmbedding-371b07a51769c-Date-2022-12-23_Time-06-32-15.log
## If there is an issue, please report to github with logFile!
## Getting UMAP Embedding
## ColorBy = GeneScoreMatrix
## Getting Matrix Values...
## 2022-12-23 06:32:17 :
## 
## Plotting Embedding
## 1 2 3 4 5 6 7 8 9 
## ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-371b07a51769c-Date-2022-12-23_Time-06-32-15.log

To plot a specific gene, we can subset this plot list:

p$CD14

To plot all genes we can use cowplot to arrange the various marker genes into a single plot.

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()
    )
})
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
## `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
## `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
## `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
## `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
## `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
## `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
## `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
## `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
do.call(cowplot::plot_grid, c(list(ncol = 3),p2))

To save an editable vectorized version of this plot, we use the plotPDF() function.

plotPDF(plotList = p, 
    name = "Plot-UMAP-Marker-Genes-WO-Imputation.pdf", 
    ArchRProj = projHeme2, 
    addDOC = FALSE, width = 5, height = 5)
## Plotting Ggplot!
## Plotting Ggplot!
## Plotting Ggplot!
## Plotting Ggplot!
## Plotting Ggplot!
## Plotting Ggplot!
## Plotting Ggplot!
## Plotting Ggplot!
## Plotting Ggplot!