Also, I really like your devolcalno plot, shown here:
image
in these cases, you only show the label of some genes rather than all. How do you plot it?(I did not find tunable parameters in the plot function)
And what is the parameter setting for certain gene expression plot in tsne?(sorry for thousands of Qs...)
The DE volcano plots in our publication were generated manually with ggplot2 and without labels. I have tried coming up with some automated settings to produce a similar result, but it was actually quite difficult and I was unable to find a way to do this for all results. I generated an interactive ggplot2 that was labelled to guide my annotation of this plot.
To make the apoptosis genes more visible, they were overplotted onto the main scatter.
As requested by @MichaelPeibo in #14:
And what is the parameter setting for certain gene expression plot in tsne?(sorry for thousands of Qs...)
The DE volcano plots in our publication were generated manually with ggplot2 and without labels. I have tried coming up with some automated settings to produce a similar result, but it was actually quite difficult and I was unable to find a way to do this for all results. I generated an interactive ggplot2 that was labelled to guide my annotation of this plot.
To make the apoptosis genes more visible, they were overplotted onto the main scatter.
I may add a tutorial for this at a later stage.