update links to docs

README.Rmd

@@ -55,20 +55,34 @@ devtools::install_github("slowkow/hlabud")
 
 # Examples
 
-See the [usage examples](vignettes/articles/examples.md) to get some ideas for how to use hlabud in your analyses.
+See the [usage examples](https://slowkow.github.io/hlabud/articles/examples.html) to get some ideas for how to use hlabud in your analyses.
 
-- [Get a one-hot encoded matrix for all HLA-DRB1 alleles](https://github.com/slowkow/hlabud/blob/main/vignettes/articles/examples.md#get-a-one-hot-encoded-matrix-for-all-hla-drb1-alleles)
-- [Convert genotypes to a dosage matrix](https://github.com/slowkow/hlabud/blob/main/vignettes/articles/examples.md#convert-genotypes-to-a-dosage-matrix)
-- [Logistic regression association for amino acid positions](https://github.com/slowkow/hlabud/blob/main/vignettes/articles/examples.md#logistic-regression-association-for-amino-acid-positions)
-- [UMAP embedding of 3,516 HLA-DRB1 alleles](https://github.com/slowkow/hlabud/blob/main/vignettes/articles/examples.md#umap-embedding-of-3516-hla-drb1-alleles)
-- [Download and unpack all data from the latest IMGTHLA release](https://github.com/slowkow/hlabud/blob/main/vignettes/articles/examples.md#download-and-unpack-all-data-from-the-latest-imgthla-release)
+- [Get a one-hot encoded matrix for all HLA-DRB1 alleles](https://slowkow.github.io/hlabud/articles/examples.html#get-a-one-hot-encoded-matrix-for-all-hla-drb1-alleles)
 
-<a href="vignettes/articles/examples.md#logistic-regression-association-for-amino-acid-positions">
+- [Convert genotypes to a dosage matrix](https://slowkow.github.io/hlabud/articles/examples.html#convert-genotypes-to-a-dosage-matrix)
+
+- [Logistic regression association for amino acid positions](https://slowkow.github.io/hlabud/articles/examples.html#logistic-regression-association-for-amino-acid-positions)
+
+- [UMAP embedding of 3,516 HLA-DRB1 alleles](https://slowkow.github.io/hlabud/articles/examples.html#umap-embedding-of-3516-hla-drb1-alleles)
+
+- [Get HLA allele frequencies from Allele Frequency Net Database (AFND)](https://slowkow.github.io/hlabud/articles/examples.html#get-hla-allele-frequencies-from-allele-frequency-net-database-afnd)
+
+- [Compute HLA divergence with the Grantham distance matrix](https://slowkow.github.io/hlabud/articles/examples.html#compute-hla-divergence-with-the-grantham-distance-matrix)
+
+- [Download and unpack all data from the latest IMGTHLA release](https://slowkow.github.io/hlabud/articles/examples.html#download-and-unpack-all-data-from-the-latest-imgthla-release)
+
+<a href="https://slowkow.github.io/hlabud/articles/examples.html#logistic-regression-association-for-amino-acid-positions">
 <img width="49%" src="vignettes/articles/examples_files/figure-html/glm-volcano-1.png">
 </a>
-<a href="vignettes/articles/examples.md#umap-embedding-of-3516-hla-drb1-alleles">
+<a href="https://slowkow.github.io/hlabud/articles/examples.html#umap-embedding-of-3516-hla-drb1-alleles">
 <img width="49%" src="vignettes/articles/examples_files/figure-html/umap-2digit-1.png">
 </a>
+<a href="https://slowkow.github.io/hlabud/articles/examples.html#get-hla-allele-frequencies-from-allele-frequency-net-database-afnd">
+<img width="49%" src="vignettes/articles/examples_files/figure-html/afnd_dqb1_02_01-1.png">
+</a>
+<a href="https://slowkow.github.io/hlabud/articles/visualize-hla-structure.html">
+<img width="49%" src="https://github.com/slowkow/ggrepel/assets/209714/4843a850-a4fd-4832-9600-0b8e9c1bb904">
+</a>
 
 # Citation
 

README.md

@@ -57,26 +57,43 @@ devtools::install_github("slowkow/hlabud")
 
 # Examples
 
-See the [usage examples](vignettes/articles/examples.md) to get some
-ideas for how to use hlabud in your analyses.
+See the [usage
+examples](https://slowkow.github.io/hlabud/articles/examples.html) to
+get some ideas for how to use hlabud in your analyses.
 
 -   [Get a one-hot encoded matrix for all HLA-DRB1
-    alleles](https://github.com/slowkow/hlabud/blob/main/vignettes/articles/examples.md#get-a-one-hot-encoded-matrix-for-all-hla-drb1-alleles)
+    alleles](https://slowkow.github.io/hlabud/articles/examples.html#get-a-one-hot-encoded-matrix-for-all-hla-drb1-alleles)
+
 -   [Convert genotypes to a dosage
-    matrix](https://github.com/slowkow/hlabud/blob/main/vignettes/articles/examples.md#convert-genotypes-to-a-dosage-matrix)
+    matrix](https://slowkow.github.io/hlabud/articles/examples.html#convert-genotypes-to-a-dosage-matrix)
+
 -   [Logistic regression association for amino acid
-    positions](https://github.com/slowkow/hlabud/blob/main/vignettes/articles/examples.md#logistic-regression-association-for-amino-acid-positions)
+    positions](https://slowkow.github.io/hlabud/articles/examples.html#logistic-regression-association-for-amino-acid-positions)
+
 -   [UMAP embedding of 3,516 HLA-DRB1
-    alleles](https://github.com/slowkow/hlabud/blob/main/vignettes/articles/examples.md#umap-embedding-of-3516-hla-drb1-alleles)
+    alleles](https://slowkow.github.io/hlabud/articles/examples.html#umap-embedding-of-3516-hla-drb1-alleles)
+
+-   [Get HLA allele frequencies from Allele Frequency Net Database
+    (AFND)](https://slowkow.github.io/hlabud/articles/examples.html#get-hla-allele-frequencies-from-allele-frequency-net-database-afnd)
+
+-   [Compute HLA divergence with the Grantham distance
+    matrix](https://slowkow.github.io/hlabud/articles/examples.html#compute-hla-divergence-with-the-grantham-distance-matrix)
+
 -   [Download and unpack all data from the latest IMGTHLA
-    release](https://github.com/slowkow/hlabud/blob/main/vignettes/articles/examples.md#download-and-unpack-all-data-from-the-latest-imgthla-release)
+    release](https://slowkow.github.io/hlabud/articles/examples.html#download-and-unpack-all-data-from-the-latest-imgthla-release)
 
-<a href="vignettes/articles/examples.md#logistic-regression-association-for-amino-acid-positions">
+<a href="https://slowkow.github.io/hlabud/articles/examples.html#logistic-regression-association-for-amino-acid-positions">
 <img width="49%" src="vignettes/articles/examples_files/figure-html/glm-volcano-1.png">
 </a>
-<a href="vignettes/articles/examples.md#umap-embedding-of-3516-hla-drb1-alleles">
+<a href="https://slowkow.github.io/hlabud/articles/examples.html#umap-embedding-of-3516-hla-drb1-alleles">
 <img width="49%" src="vignettes/articles/examples_files/figure-html/umap-2digit-1.png">
 </a>
+<a href="https://slowkow.github.io/hlabud/articles/examples.html#get-hla-allele-frequencies-from-allele-frequency-net-database-afnd">
+<img width="49%" src="vignettes/articles/examples_files/figure-html/afnd_dqb1_02_01-1.png">
+</a>
+<a href="https://slowkow.github.io/hlabud/articles/visualize-hla-structure.html">
+<img width="49%" src="https://github.com/slowkow/ggrepel/assets/209714/4843a850-a4fd-4832-9600-0b8e9c1bb904">
+</a>
 
 # Citation
 

index.Rmd

@@ -1,6 +1,6 @@
 # hlabud: HLA analysis in R <img width="25%" align="right" src="https://github.com/slowkow/hlabud/assets/209714/b39a3f04-c9a8-4867-a3e0-9434f0f9ef20"></img>
 
-hlabud provides methods for retrieving sequence alignment data from the [IMGTHLA] database and converting the data into R matrices ready for downstream analysis. The [vignette](articles/examples.html) shows examples of how to use the data with logistic regression and dimensionality reduction.
+hlabud provides methods to retrieve sequence alignment data from [IMGTHLA] and convert the data into convenient R matrices ready for downstream analysis. See the [usage examples](https://slowkow.github.io/hlabud/articles/examples.html) to learn how to use the data with logistic regression and dimensionality reduction. We also share tips on how to [visualize the 3D molecular structure](https://slowkow.github.io/hlabud/articles/visualize-hla-structure.html) of HLA proteins and highlight specific amino acid residues.
 
 [IMGTHLA]: https://github.com/ANHIG/IMGTHLA
 
@@ -45,12 +45,18 @@ See the [usage examples](articles/examples.html) to get some ideas for how to us
 
 - [Download and unpack all data from the latest IMGTHLA release](articles/examples.html#download-and-unpack-all-data-from-the-latest-imgthla-release)
 
-<a href="articles/examples.html#logistic-regression-association-for-amino-acid-positions">
+<a href="https://slowkow.github.io/hlabud/articles/examples.html#logistic-regression-association-for-amino-acid-positions">
 <img width="49%" src="articles/examples_files/figure-html/glm-volcano-1.png">
 </a>
-<a href="articles/examples.html#umap-embedding-of-3516-hla-drb1-alleles">
+<a href="https://slowkow.github.io/hlabud/articles/examples.html#umap-embedding-of-3516-hla-drb1-alleles">
 <img width="49%" src="articles/examples_files/figure-html/umap-2digit-1.png">
 </a>
+<a href="https://slowkow.github.io/hlabud/articles/examples.html#get-hla-allele-frequencies-from-allele-frequency-net-database-afnd">
+<img width="49%" src="articles/examples_files/figure-html/afnd_dqb1_02_01-1.png">
+</a>
+<a href="https://slowkow.github.io/hlabud/articles/visualize-hla-structure.html">
+<img width="49%" src="https://github.com/slowkow/ggrepel/assets/209714/4843a850-a4fd-4832-9600-0b8e9c1bb904">
+</a>
 
 
 Citation

index.md

@@ -1,10 +1,13 @@
 # hlabud: HLA analysis in R <img width="25%" align="right" src="https://github.com/slowkow/hlabud/assets/209714/b39a3f04-c9a8-4867-a3e0-9434f0f9ef20"></img>
 
-hlabud provides methods for retrieving sequence alignment data from the
-[IMGTHLA](https://github.com/ANHIG/IMGTHLA) database and converting the
-data into R matrices ready for downstream analysis. The
-[vignette](articles/examples.html) shows examples of how to use the data
-with logistic regression and dimensionality reduction.
+hlabud provides methods to retrieve sequence alignment data from
+[IMGTHLA](https://github.com/ANHIG/IMGTHLA) and convert the data into
+convenient R matrices ready for downstream analysis. See the [usage
+examples](https://slowkow.github.io/hlabud/articles/examples.html) to
+learn how to use the data with logistic regression and dimensionality
+reduction. We also share tips on how to [visualize the 3D molecular
+structure](https://slowkow.github.io/hlabud/articles/visualize-hla-structure.html)
+of HLA proteins and highlight specific amino acid residues.
 
 For example, let’s consider a simple question about two HLA genotypes
 DRB1\*04:174 and DRB1\*15:152. What amino acid positions are different
@@ -54,12 +57,18 @@ how to use hlabud in your analyses.
 -   [Download and unpack all data from the latest IMGTHLA
     release](articles/examples.html#download-and-unpack-all-data-from-the-latest-imgthla-release)
 
-<a href="articles/examples.html#logistic-regression-association-for-amino-acid-positions">
+<a href="https://slowkow.github.io/hlabud/articles/examples.html#logistic-regression-association-for-amino-acid-positions">
 <img width="49%" src="articles/examples_files/figure-html/glm-volcano-1.png">
 </a>
-<a href="articles/examples.html#umap-embedding-of-3516-hla-drb1-alleles">
+<a href="https://slowkow.github.io/hlabud/articles/examples.html#umap-embedding-of-3516-hla-drb1-alleles">
 <img width="49%" src="articles/examples_files/figure-html/umap-2digit-1.png">
 </a>
+<a href="https://slowkow.github.io/hlabud/articles/examples.html#get-hla-allele-frequencies-from-allele-frequency-net-database-afnd">
+<img width="49%" src="articles/examples_files/figure-html/afnd_dqb1_02_01-1.png">
+</a>
+<a href="https://slowkow.github.io/hlabud/articles/visualize-hla-structure.html">
+<img width="49%" src="https://github.com/slowkow/ggrepel/assets/209714/4843a850-a4fd-4832-9600-0b8e9c1bb904">
+</a>
 
 # Citation
 

vignettes/articles/visualize-hla-structure.Rmd

@@ -38,7 +38,7 @@ HLA-DR 3pdo
 
 Also try searching the PDB website for, e.g., `"HLA-DR"` and see if there is a more appropriate structure for your analysis.
 
-# NGLVieweR
+# Using NGLVieweR
 
 Let's try to visualize position 9 in the HLA-B protein structure.
 
@@ -120,7 +120,7 @@ What fraction of reported HLA-B alleles have Tyr9?
 sum(a$onehot[,"pos9_Y"] == 1) / nrow(a$onehot)
 ```
 
-# PyMOL
+# Using PyMOL
 
 [PyMOL] is one of my favorite methods for visualizing protein structures, because it allows us to [change a residue][mutagenesis] in an existing protein and visualize the new mutated protein.
 
@@ -189,5 +189,6 @@ R:
 
 * https://www.raymolecule.com
 
+[PyMOL]: https://pymol.org
 [mutagenesis]: https://pymolwiki.org/index.php/Mutagenesis