To reduce the number of labeled genes on your graph, you could choose a more stringent cutoff for the labeling. For example, instead of labeling genes with p values below 0.05, you can plot those that have an absolute logFC higher than 1 or 2 or 3 ... whatever. At the end, it's up to you. You have to think what is important to show with this graph and what should be the message that you sent with this graph. BTW, your question in comments is beyond the question of this post ;)

Do it before ggplot to create a subset of your dataframe final_tumor and then replace final_tumor by rep_final in the ggplot command

you can use sample function to select random rows of your dataframe: rep_final = final_tumor[sample(1:nrow(final_tumor), size = 1000), ]

How long is your dataset ? Maybe it is not relevant to plot all genes. Maybe, you can plot a representative part of your dataset (e.g. 2000 randomly selected genes). Regarding EnhancedVolcano, I do not have experience with it. Sorry.

Yes, either one or two of your biological replicate is different from others, or you have two subpopulations in all of your replicate. I think, you can try to plot their densities separately to see how values of each replicate is distributed. Either, they are all single peak but with different means (which after merging create two peaks), or each replicate have two peaks.

Could potentially be two subpopulations of the GMP group...

If you have 16 for each conditions, you should associate them in a single dataframe and plot a boxplot or a violin plot as advised by @haci.

Totally agree ;) and personally, I won't publish those kind of results (at least in this format). But it's well beyond the scope of the question :D

I agree if you are able to have more than 3 replicates. Otherwise, the spread observed with boxplot or violin plot won't mean a lot. But as it seems that individual values are the count of different cell types from single cell RNA seq, I doubt you can have a lot of replicates. That's why I advised for barchart. But it is also possible to plot individual values and the mean using geom_pointrange.

Ok, so your question is about to calculate len and sd ? because you don't have these values, right ? For your account, you can see this link: bioinformatics.stackexchange.com/help/merging-accounts. Also, when you are registered on one site of StackExchange, you can directly create a new account on another StackExchange website by clicking on topright join Community button, it will automatically link your account on all sites you are registered of.

In your exemple, there is no mention of len and sd, so it is not clear what are these values and how you want to calculate them. Also, does the related question is yours ? because you don't have the same username ?