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Monocle3 - gene expression dot plot (ggplot2 equivalent)

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:

monocle3 gene expression dot plot

Desired:

monocle3 desired dot plot

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.

monocle3 ggplot2 data-visualization
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updated by gglim • gglim • written by seattlescientist_01 • seattlescientist_01

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)

• 0 views • link
written by fracarb8 fracarb8

agree with fracarb8 , you just need to set proper colour & transparency

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written by gglim • gglim

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