FeaturePlot on a KDE Plot/density plot
Entering edit mode
2.7 years ago
fouerghi20 ▴ 70

I created a KDE plot (density plot) using the following code:

contplus <- data.frame(scADAR$tsne@cell.embeddings)
tSNE_1 <- scADAR$tsne@cell.embeddings[,1]
tSNE_2 <- scADAR$tsne@cell.embeddings[,2]

# Initialize arrays for data subsets for each condition and for plots 
plotData <- list()
modGalaxyPlot <- list()

# Take each subset of data and generate a plot 

# Use grep to subset the data 
plotData[[1]] <- contplus[grepl(as.numeric(1), rownames(contplus)),]

# Generate galaxy plot for each condition
modGalaxyPlot[[1]] <- ggplot(plotData[[1]], aes(tSNE_1, tSNE_2)) +
  stat_density_2d(aes(fill = ..density..), geom = 'raster', contour = FALSE) +
  scale_fill_viridis(option = "magma") +
  coord_cartesian(expand = FALSE, xlim = c(min(tSNE_1), max(tSNE_1)), ylim = c(min(tSNE_2),max(tSNE_2))) +
  geom_point(shape = '.', col = 'white') 

# to visualize one of the two plots

I was wondering if it would be possible to highlight a density plot with certain genes. I basically want to do what FeaturePlot does but on a KDE plot and I am not sure how to adapt my code to do that.

single cell seurat r RNA-Seq • 777 views

Login before adding your answer.

Traffic: 1295 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6