setup and usages were updated.

Author: KunDHuang

README.md

@@ -4,8 +4,8 @@ Computational workflows for reproducing analysis in the study of Huang et al., 2
 ![Graphical abstract](./images/graphical_abstract.jpg)
 
 #### Table of contents
-1. [Setup]()
-2. [General usage]()
+1. [Setup](./docs/setup_general_usage.md)
+2. [General usage](./docs/setup_general_usage.md)
 3. Detailed tutorials
     * [Reads quality inspection with cumulative distribution function](./docs/cumulative_distribution_function.md)
     * [Alpha diversity analysis](./docs/alpha_diversity_analysis.md)
@@ -14,4 +14,5 @@ Computational workflows for reproducing analysis in the study of Huang et al., 2
     * [ComplexHeatmap plotting](./docs/make_ComplexHeatmap.md)
     * [Make mosaic plot](./docs/make_mosaic_plot.md)
     * [Machine learning analysis](./docs/machine_learning_analysis.md)
-    * [Deviation plot, UpSet plot, Lollipop plot](./docs/several_plots.md)
+    * [Deviation plot, UpSet plot, Lollipop plot](./docs/several_plots.md)
+

docs/setup_general_usage.md

@@ -0,0 +1,45 @@
+## First time setup
+
+While no pre-installation is required for running workflows in this repository, you first need to download the repository to your local computer:
+~~~bash
+git clone https://github.com/KunDHuang/KunDH-2024-CRM-MSM_metagenomics.git
+~~~ 
+
+NOTE: As scripts provided in this repository depend on many third-party tools, we highly recommend [conda](https://conda.io/projects/conda/en/latest/index.html) environment for managing required dependencies which are listed in each of sections in the tutorials.
+
+## General usages
+
+This repository provides two types of utilities: 1) Python scripts and 2) Importable R functions
+
+1) Python scripts are codes encapulated for executing specific analysis.
+Example: [visualizing cumulative distribution function.](../docs/cumulative_distribution_function.md)
+~~~bash
+$ cumulative_distribution_function.py --input_table <example_reads_stats.tsv> --output_figure <nr_QC_reads_pairs.svg> --value_header <nr_QC_reads_pairs> --palette_map <reads_stats_color_map.tsv>
+~~~  
+
+2) Importable R functions are R codes wrapped up for solving specific problems and should be reusable by just importing their scripts. 
+
+Example: [estimate PERMANOVA significance.](../docs/beta_diversity_analysis.md)
+
+~~~R
+>source(file = "path_to_the_package/KunDH-2023-CRM-MSM_metagenomics/scripts/functions/beta_diversity_funcs.R")
+>est_permanova(mat = matrix, 
+               md = metadata, 
+               variable = "condom_use", 
+               covariables = c("Antibiotics_6mo", "HIV_status", "inflammatory_bowel_disease", "BMI_kg_m2_WHO", "diet"),
+               nper = 999, 
+               to_rm = c("no_receptive_anal_intercourse"),
+               by_method = "margin")
+
+                           Df SumOfSqs      R2      F Pr(>F)   
+condom_use                  4   1.2161 0.08194 1.5789  0.008 **
+Antibiotics_6mo             2   0.4869 0.03281 1.2643  0.160   
+HIV_status                  1   0.3686 0.02484 1.9146  0.030 * 
+inflammatory_bowel_disease  1   0.2990 0.02015 1.5529  0.066 . 
+BMI_kg_m2_WHO               5   1.8376 0.12382 1.9087  0.002 **
+diet                        3   0.8579 0.05781 1.4853  0.036 * 
+Residual                   49   9.4347 0.63571                 
+Total                      65  14.8412 1.00000                 
+---
+Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
+~~~