Improve READMEs

- Add links to ASV tables
- Put links to analysis outputs with their descriptions in
  analysis/README.md
- Improve descriptions of files in analysis/README.md

README.md

@@ -2,30 +2,33 @@
 
 This repository contains the microbiome data analysis for the manuscript
 
-R. Thanissery, M.R. McLaren, A. Rivera, A. Reed, N.S. Betrapally, T. Burdette,
-J.A. Winston, M. Jacob, B.J. Callahan, and C.M. Theriot (2019).
-Characterization of _C. difficile_ strains isolated from domestic animals and
-the associated changes in the host fecal microbiota. (Submitted)
+Thanissery R, McLaren MR, Rivera A, Reed AD, Betrapally NS, Burdette T, Winston
+JA, Jacob M, Callahan BJ, Theriot CM. 2019. Characterization of _C. difficile_
+strains isolated from companion animals and the associated changes in the host
+fecal microbiota. bioRxiv 822577. doi:10.1101/822577
 
 The raw sequence reads are available at
 <https://www.ncbi.nlm.nih.gov/bioproject/PRJNA562547>. The results of
 bioinformatic analysis of the raw reads with DADA2, including taxonomy
 assignment against Silva v132 using DADA2's `assignTaxonomy()` and
-`addSpecies()` functions are in `results/dada2`, and as a phyloseq object in
-`results/ps.Rds`.
+`addSpecies()` functions are in [results/dada2](results/dada2), and as a
+phyloseq object in [results/ps.Rds](results/ps.Rds).
 
-All bioinformatic and statistical analyses are contained in R-markdown
-documents in `analysis/`. A description of these files is given in
-[analysis/README.md](analysis/README.md). For most analyses, versions that are
-already rendered to html files are included and can be viewed by clicking on
-the following links,
+The results/ folder also includes plain-text (.csv format) tables mapping ASV
+names to their amplicon sequence and taxonomy. These tables can be viewed
+directly in a web browser by clicking the below links.
+
+* [Table of all ASV sequences](results/all-asv-sequences-and-taxonomy.csv)
+* [Table of select ASV
+  sequences](results/select-asv-sequences-and-taxonomy.csv) (all
+  _Clostridiodes_ ASVs, all _Clostridium hiranonis_ ASVs, and ASVs shown in
+  Figure 3)
+* [Table of ASV
+  sequences explicitly mentioned in the
+  manuscript](results/manuscript-asv-sequences-and-taxonomy.csv) (Excludes
+  low-prevalence _C. hiranonis_ ASVs)
 
-* [00-sample-data.html](https://rthanis.github.io/animal-cdiff/analysis/00-sample-data.html)
-* [03-taxonomy.html](https://rthanis.github.io/animal-cdiff/analysis/03-taxonomy.html)
-* [alpha-beta.html](https://rthanis.github.io/animal-cdiff/analysis/alpha-beta.html)
-* [alpha-beta-no-cdiff.html](https://rthanis.github.io/animal-cdiff/analysis/alpha-beta-no-cdiff.html)
-* [canine-aldex.html](https://rthanis.github.io/animal-cdiff/analysis/canine-aldex.html)
-* [cdiff-asvs.html](https://rthanis.github.io/animal-cdiff/analysis/cdiff-asvs.html)
-* [cdiff-vs-age.html](https://rthanis.github.io/animal-cdiff/analysis/cdiff-vs-age.html)
-* [hiranonis-asvs.html](https://rthanis.github.io/animal-cdiff/analysis/hiranonis-asvs.html)
-* [multivariate-regression.html](https://rthanis.github.io/animal-cdiff/analysis/multivariate-regression.html)
+All bioinformatic and statistical analyses are contained in R-markdown
+documents in [analysis/](analysis/). A description of these files and links to
+rendered versions showing all numerical output and figures is given in
+[analysis/README.md](analysis/README.md).

analysis/README.md

@@ -13,6 +13,9 @@ saves the cleaned version in `results/metadata-clean.csv` and
 `results/metadata-clean.Rds`; the latter includes formatting of some variables
 as factors.
 
+Rendered version:
+[00-sample-data.html](https://rthanis.github.io/animal-cdiff/analysis/00-sample-data.html)
+
 #### 01-dada2.Rmd
 
 This script runs the DADA2 pipeline to analyze the 16S sequence data and create
@@ -34,38 +37,70 @@ and C. scindens, which were not identified in the initial species assignment.
 The results are saved in `results/hiranonis-and-scindens.csv` and added to the
 taxonomy table in the phyloseq object.
 
+Rendered version:
+[03-taxonomy.html](https://rthanis.github.io/animal-cdiff/analysis/03-taxonomy.html)
+
 ## Statistical analysis
 
+### Community-wide analyses
+
+#### alpha-beta.Rmd
+
+This script analyses patterns of alpha and beta diversity across animal host
+types, and between C. difficile positive and negative samples within an animal
+host type. Alpha and beta diversities were computed with C. difficile reads
+included or excluded, giving approximately indistinguishable results.
+
+Rendered version:
+[alpha-beta.html](https://rthanis.github.io/animal-cdiff/analysis/alpha-beta.html)
+
+Rendered version with C. difficle reads removed:
+[alpha-beta-no-cdiff.html](https://rthanis.github.io/animal-cdiff/analysis/alpha-beta-no-cdiff.html)
+
+#### canine-aldex.Rmd
+
+This script performs a compositional PCA analysis and community-wide
+differential-abundance test to look for ASVs associated with C. difficile
+presence.
+
+Rendered version:
+[canine-aldex.html](https://rthanis.github.io/animal-cdiff/analysis/canine-aldex.html)
+
+### C. difficile specific analyses
+
 #### cdiff-vs-age.Rmd
 
 This script visualizes C. difficile presence by lab sporulation assay versus
 age.
 
+Rendered version:
+[cdiff-vs-age.html](https://rthanis.github.io/animal-cdiff/analysis/cdiff-vs-age.html)
+
 #### cdiff-asvs.Rmd
 
-This script examines the co-occurrance of the three C. difficile ASVs and
+This script examines the co-occurrence of the three C. difficile ASVs and
 compares the detection of C. difficile by lab sporulation assay to that via 16S
 community sequencing.
 
-#### cross-host-alpha-beta.Rmd
-
-This script analyses patterns of alpha and beta diversity across animal host
-types, and between C. difficile positive and negative samples within an animal
-host type.
-
-#### canine-aldex.Rmd
+Rendered version:
+[cdiff-asvs.html](https://rthanis.github.io/animal-cdiff/analysis/cdiff-asvs.html)
 
-This script performs a compositional PCA analysis and community-wide
-differential-abundance test to look for ASVs associated with C. difficile
-presence.
+### Analyses of C. hiranonis and its relationship with C. difficile 
 
 #### hiranonis-asvs.Rmd
 
-This script analyses the co-abundance patterns of the various C. hiranonis
-ASVs.
+This script analyses the prevalence of C. hiranonis, the association of C.
+hiranonis presence with C. difficile, and the co-abundance patterns of the
+various C. hiranonis ASVs.
+
+Rendered version: 
+[hiranonis-asvs.html](https://rthanis.github.io/animal-cdiff/analysis/hiranonis-asvs.html)
 
 #### multivariate-regression.Rmd
 
 This script performs logistic regression of C. difficile presence versus
 presence of the two C. hiranonis types, with and without the sample covariates
 of age, antibiotics use, GI distress, and sex.
+
+Rendered version:
+[multivariate-regression.html](https://rthanis.github.io/animal-cdiff/analysis/multivariate-regression.html)