Question: Normalization to fit bars on GraPhlAn generated cladogram
gravatar for shibl_a
8 months ago by
shibl_a20 wrote:


I recently generated a cladogram on GraPhlAn from my Metaphlan2 output and wanted to add a ring displaying the relative abundances of each clade. I created a text file with this information according to the example ( The issue is that my dataset (the 20 most abundant clades) is mainly dominated by one clade (83%, and the next most abundant is at 11% then 3% all the way down to 0.00173%) and therefore the image looks ridiculous (one giant bar from one place and the rest are basically invisible). My question is; what's the best way I can normalize these numbers so I get a reasonable range that would display the true abundances of the clades on the figure? any ideas?


ADD COMMENTlink modified 4 months ago by francesco.asnicar0 • written 8 months ago by shibl_a20
gravatar for francesco.asnicar
4 months ago by
francesco.asnicar0 wrote:

Hi, one way is to use the log1p from numpy ( of the relative abundances, in your case:

>>> np.log1p(83)
>>> np.log1p(11)
>>> np.log1p(3)
>>> np.log1p(0.00173)
ADD COMMENTlink written 4 months ago by francesco.asnicar0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1958 users visited in the last hour