Question: (Closed) Very low probability densities
gravatar for rishi
6 weeks ago by
rishi10 wrote:


I'm generating a density plot using the ggplot2 library:

ggplot(df_chr20, aes(x=start1)) + geom_density() + theme_bw() 
ggplot(df_chr21, aes(x=start1)) + geom_density() + theme_bw()

The data frame for df_chr20 has 1573 rows, and I wanted to plot the probability density of genomic regions as x = start1. The same for df_chr21, with 1271 rows. What I see in the plot is what I expect, but is there a reason why the y-axis probablilty densities are so low? The area under the curve is surely not equal to 1.

I expected the high localised high density in chr 21, and both the plots have similar scales in terms of y-axis values. But since they are so low, how can I interpret this plot?

I found some information here, but my values are much lower than the examples.

Any help would b every kind!

enter image description here

If the plot isn't visible, please click here or the link:

R • 131 views
ADD COMMENTlink modified 6 weeks ago by Biostar ♦♦ 20 • written 6 weeks ago by rishi10

Why do you think they are low? Your chromosome has millions of bases, but you only have values for about a thousand of them. In other words, most values are 0, so the average should be very low.

ADD REPLYlink written 6 weeks ago by igor11k

Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)

ADD REPLYlink written 6 weeks ago by RamRS27k

Hello rishi!

It appears that your post has been cross-posted to another site:

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 6 weeks ago by RamRS27k

Hello rishi!

We believe that this post does not fit the main topic of this site.

Asked and answered here: OP, please don't do this, it's immensely disrespectful and annoying.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.


ADD REPLYlink written 6 weeks ago by RamRS27k
Please log in to add an answer.
The thread is closed. No new answers may be added.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1021 users visited in the last hour