Density vs gene count plot

Question

[dpc]

Hi there!!! I am posting this query with respect to this article. In the supplementary figure section they have provided a Density vs gene number plot in figure 2.a and 2.b. Can anyone tell me what this "Density" refers to?

thanks, DC7

Answer 1

[antonioggsousa]

Hi,

From what I understood the density in Fig. 2A is the frequency, i.e., the no. of times or no. of reads, of each gene. Since the density is in the order of 3e-06, my guess is that the frequency/density is in proportion/relative abundance rather than absolute counts. So, what the plots show is how many genes have 10 reads, how many have 1000, how many have 10 K reads and so on, but in proportion - this is my guess - it's not clear from the legend's description. So it shows the distribution of gene counts.

The density in Fig. 2B is a bit different. So, is the frequency, i.e., how many genes have a specific p-value, on the x-axis.

I hope this helps,

António

[dpc]

Thanks Antonio. It was really helpful. Do you know which software or R-package can be used for that?

Thanks, Deep

[antonioggsousa]

In R, you can use the R-base functions such as hist() or density() or you can use the R package ggplot2. Have a look into this STHDA tutorial.

António