Color correction in gneiss balance-taxonomy

Ravenclaw · November 29, 2018, 1:40pm

Hi
In the output for gneiss balance-taxonomy, the colors used for the different categories are switched in the log ratio plot and the proportion plot. Here is an example. Its a minor thing but could be confusing. Im using 2018.8
Cheers

mortonjt · November 29, 2018, 4:41pm

We’re deprecating all of the visualizations in gneiss by the next release - so this won’t be a concern in the future release.

The recommendation for future analyses is to export the results to either Python or R to make custom results. There will be tutorials posted shortly on how to do that.

saatkinson · September 19, 2019, 9:46pm

Hello @mortonjt

I’m working with gneiss in version 2019.7 and I was wondering about the status of tutorials to make custom results figures in python and/or R mentioned above. Any news?

Thanks,
Samantha

mortonjt · October 25, 2019, 2:21am

HI @saatkinson, we have some tutorials on how to manipulate these balances in python.
See these tutorials: https://biocore.github.io/gneiss/docs/v0.4.0/index.html

There isn’t a tutorial for the proportion plots yet - but there are some notebooks below where these plots were originally developed

github.com

knightlab-analyses/american-gut-analyses/blob/master/ipynb/core-balance-classifier.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Here we will create balance classifiers to identify differences due to plant diet and country.\n",
    "\n",
    "Make sure that the appropriate files are downloaded.  They can be obtained from the ftp link using the following commands\n",
    "\n",
    "```bash\n",
    "wget ftp://ftp.microbio.me/AmericanGut/manuscript-package/1250/deblur_125nt_no_blooms.biom\n",
    "\n",
    "wget ftp://ftp.microbio.me/AmericanGut/manuscript-package/1250/ag_map_with_alpha.txt\n",
    "```\n",
    "\n",
    "Also load the correct environment.  That can be done with\n",
    "\n",
    "```bash\n",
    "conda env create -n balance-analysis -f env/gneiss-0.4.1.txt\n",

This file has been truncated. show original

github.com

knightlab-analyses/american-gut-analyses/blob/master/ipynb/western-nonwestern-balances.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Here we will create balance classifiers to identify differences due to plant diet and country.\n",
    "\n",
    "Make sure that the appropriate files are downloaded.  They can be obtained from the ftp link using the following commands\n",
    "\n",
    "```bash\n",
    "wget ftp://ftp.microbio.me/AmericanGut/manuscript-package/1250/deblur_125nt_no_blooms.biom\n",
    "\n",
    "wget ftp://ftp.microbio.me/AmericanGut/manuscript-package/1250/ag_map_with_alpha.txt\n",
    "```\n",
    "\n",
    "Also load the correct environment.  That can be done with\n",
    "\n",
    "```bash\n",
    "conda env create -n balance-analysis -f env/gneiss-0.4.1.txt\n",

This file has been truncated. show original

We do have docs here on how to generate the proportions plots here. It doesn’t look like those are being rendered correctly, so that needs to be corrected in the next release.