From 0ee526dada41275d6f930c6ecfe074f1503ad695 Mon Sep 17 00:00:00 2001 From: Jim Shaw Date: Sat, 17 Aug 2024 20:41:45 -0700 Subject: [PATCH 1/2] Update README.md --- README.md | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 5c32088d..6c99bd9b 100644 --- a/README.md +++ b/README.md @@ -4,24 +4,30 @@ In the scripts/* folder you will find a set of python scripts for recreating res For example, `python scripts/chng_between_sample.py` will regenerate the figures for the skin microbiome fungi result in our paper. +For files that are gzipped, you may have to ungzip. + ### Fig. 1 * Look at `scripts/synthetic_pois_plot.py` ### Fig. 2 -* Look at `profile_analysis.ipynb` +* Look at `profile_analysis.ipynb`. ### Fig. 3 -* Look at `scripts/diagonal_ani_nn.py` and `scripts/mock_community_plot.py` +* `cd` into `real_gut_results_v0.5` and look at the `real_gut_results_v0.5/scripts` python scripts. ### Fig. 4 +* Look at `scripts/diagonal_ani_nn.py` and `scripts/mock_community_plot.py` + +### Fig. 5 + * Look at `analysis.ipynb` for the MWAS statistical calculation and `scripts/manhat.py`. * Look at `scripts/chng_between_sample.py` for the Chng et al analysis -### Fig. 5 +### Fig. 6 * Look at `real_profile_analysis.ipynb`. 1. Python 3 with the following libraries: From d943edbf90a6fed322af809efe7028d91b5b00bf Mon Sep 17 00:00:00 2001 From: Jim Shaw Date: Sat, 17 Aug 2024 20:42:34 -0700 Subject: [PATCH 2/2] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 6c99bd9b..4ed56895 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # sylph-test - scripts for recreating results from sylph paper -In the scripts/* folder you will find a set of python scripts for recreating results from Fig.1, Fig.3, Fig. 4 from our paper. The notebooks will show how Figs. 2 and 5 were obtained. All intermediate results are already present in this directory except for the following: +In the scripts/* folder you will find a set of python scripts for recreating results from Fig.1, Fig. 2, Fig.3, Fig. 4, Fig. 6 from our paper. The notebooks will show how Figs. 2 and 5 were obtained. All intermediate results are already present in this directory except for the following: For example, `python scripts/chng_between_sample.py` will regenerate the figures for the skin microbiome fungi result in our paper.