metacoder

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Error with parse_tax_data and installation issues

12

Transferred from https://github.com/ropensci/taxa/issues/210 for @emankhalaf I have a feature table with taxonomy collapsed to the genus level, where the first column is the taxonomy (ranks separated by ;), then the...

zachary-foster

Failure when installing metacoder in RStudio in both windows and Ubuntu 20.04

2

Hi, I got this error when installing metacoder in windows: devtools::install_github("grunwaldlab/metacoder") WARNING: Rtools is required to build R packages, but is not currently installed. Please download and install Rtools 4.0...

emankhalaf

Confusion about filter_taxa and filter_obs

3

Hello, Thank you for developing MetaCoder. I am enjoying the package so far. I am trying to filter my dataset before plotting heat trees, but instead of throwing counts away...

levlitichev

otu_table, tax_data and sample_data only contains NA after parsing from phyloseq

12

Hi, I am trying to parse my phyloseq object to a taxmap object but I cant get it to work properly. The parsing seems to work fine (No error message)...

FFoQS90

The taxon list table for the differential heat tree

6

Regarding the differential heat tree, how I can print the taxon list table for the differential heat tree after Wilcoxon rank Sum test? The taxon list should include the more...

biosciences

> hmp_samples Error: Corrupt `grouped_df` using old (< 0.8.0) format. ℹ Strip off old grouping with `ungroup()`. Run `rlang::last_error()` to see where the error occurred.

zachary-foster

Export p-values with heircachy amd taxanomic names?

2

Hi there! I was wondering, is there a way to export the stats generated from the heat trees? Based on your tutorial we can get the p-values for the heat...

catherineel

Alpha-diversity assessed by richness (Chao1, ACE)

2

I can see you have done alpha-diversity assessment by using Inverse Simpson index, how could I assess the alpha-diversity by richness using Chao1 and ACE?

biosciences

Comparing heat trees using presence/absence data and binomial glm

11

Hello @zachary-foster I attended your workshop at the Phytobiome Conference in Montpellier last December and I managed to realize several comparing heat trees (using a phyloseq object). Again, thanks for...

M-Ourry

`compare_groups`: allow comparisions with more than one grouping variable

5

Instead of: ```r compare_groups(obj, dataset = "tax_abund", cols = hmp_samples$sample_id, groups = paste(hmp_samples$sex, hmp_samples$body_site)) ``` allow ```r compare_groups(obj, dataset = "tax_abund", cols = hmp_samples$sample_id, groups = list(sex = hmp_samples$sex, site...

zachary-foster