Entering edit mode
10 weeks ago
It looks like if you run plot_genes_by_group function in monocle3, it generates a gene expression dot plot for expression of top marker genes per partition/cluster. But does anyone know if there is a way to perform the same type of graph using ggplot2 where the dots for 0 expression don't show up as much (hardly) and only dots for 25, 50, and 75% expression show up?
Original:
Desired:
The monocle3 software performs single-cell RNA-seq analysis on cell dataset objects so if there is some additional wrangling that needs to be performed on this object before it can be analyzed in ggplot, then that's fine with me too.
Just curious if anyone had any thoughts on this. Thanks.
Instead of recreating it yourself you can try to change the colour pallet to achieve the look you are looking for. As the function returns a ggplot object, you can use
+ scale_color_gradientn(colors = c("white","blu"))(or whatever colours)agree with fracarb8 , you just need to set proper colour & transparency