Closed zhuchcn closed 6 years ago
lch14forever
commented
6 years ago I was actually considering using only the biom package because the phyloseq package seems to be too clunky. Anyways, it also seems nice for the package to support phyloseq objects.
zhuchcn
commented
6 years ago Alright then just take it as a temporary option. Do you mean the phyloseq package is too big? I actually like the phyloseq because of its object oriented design and the convenience to DESeq2, although the graphic functions do need improvement. Look forward to see your pure biom support!
On Tue, Jun 19, 2018 at 5:18 PM Chenhao Li notifications@github.com wrote:
I was actually considering using only the biom package because the phyloseq package seems to be too clunky. Anyways, it also seems nice for the package to support phyloseq objects.
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-- Chenghao Zhu (Trevor) MS, PhD Candidate Graduate Group of Nutritional Biology (GGNB) Department of Nutrition, UC Davis 3402 Meyer Hall, Zivkovic Lab Davis, California (530)750-9372 chhzhu@ucdavis.edu
Here's what I did so far. In the clado.anno, I cheated a little bit by using the geom_point() with the size of 0, but force the legend size to be normal. I also wrote a function of parsePhyloseq based on your parseMetaphlanTSV to parse from a phyloseq object. I noticed that you have a "biom format" on your to-do list. The phyloseq package is able to import the biom file, and then we can use the parsePhyloseq to visualize it. I added some example in both the readme file and the vignette.