mortonjt
October 25, 2019, 2:21am
9
HI @saatkinson , we have some tutorials on how to manipulate these balances in python.Welcome to gneiss’s documentation! — gneiss 0.2 documentation
There isn't a tutorial for the proportion plots yet - but there are some notebooks below where these plots were originally developed
{
"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",
show original
{
"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",
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.
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