metacoder

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For very small subgraphs (1-3 nodes) some layout are not appropriate. Currently, one warning is given per invalid graph, which can result in many warnings in some cases. - [...

zachary-foster

Error in layout$fun(graph = list(1598, TRUE, c(0, 0, 0, 0, 0, 0, 0, 0, : At rinterface_extra.c:82 : The value 10.642051692927977 is not representable as an integer. Invalid value

8

Hello, I finally got through the scripts to the point where I am trying to tweak my Log2FC heat.tree I get a tree with no issues if I use the...

dhadsell

Relative abundance in heat tree

4

Hello Metacoder devs, It must be pretty straight forward but I'm having a hard time trying to plot relative abundance of the taxa in the whole dataset instead of OTU...

SimonMorvan

Phyloseq heat tree doesn't see taxon_id or supertaxon_id when trying filter_taxa?

9

Apologies if this has been discussed before or is an easy fix! I've just been introduced to metacoder and I want to be able to use a phyloseq object as...

hank00000

how to get access to the Taxmap dataframe ?

1

Hi everyone, I am trying to use metacoder to visualise differential abundance taxonomies that I have identify outside metacoder. I create a metacoder object with the full taxonomy abundance table....

mariabernard

Getting incorrectly formated results with zero_low_counts

4

Hello, I am trying to run Metacoder on some 16s data from water samples that was obtained through RTL genomics. I import 2 text files. The first contains the otu...

dhadsell

calc_diff_abund_deseq2, linear variables and "design"?

3

Dear Zachary and members of the Grunwald lab, first of all: Thank you very, very much for the metacoder heat tree package! These heat trees open up so many possibilities!...

msolbach

Hi Grunewaldlab-members and coders, thank you so much for the metacodeR package and the great documentation provided with it. I am playing with it for the last days to nicely...

kazpa-kay

Best practice to parse data from QIIME

4

Hi @zachary-foster! Thanks so much for your package! I'm trying to parse the taxonomic information output from QIIME, and I am wondering the best way to do this. With command...

jrherr

ggtext compatibility

2

Hello, I cannot find this infoirmation anywhere, but I was curious to know if there is a way to use markdown text, for example using `ggtext`, to italicize the tree...

Gian77