fix typos in docs, update makefile

Makefile

@@ -2,7 +2,12 @@
 
 # ROOT_DIR:=$(shell dirname "$(realpath $(firstword $(MAKEFILE_LIST)))")
 
-all: README.md vignettes/articles/examples.html docs/index.html vignettes/articles/visualize-hla-structure.html
+rmds := $(wildcard vignettes/articles/*.Rmd)
+articles = $(rmds:.Rmd=.html)
+css = vignettes/articles/custom.css
+mans := $(wildcard man/*.Rd)
+
+all: README.md docs/index.html
 
 clean:
 	rm -rf docs/ README_{files,cache} README.{md,html} index.{md,html} vignettes/articles/examples_{files,cache} vignettes/articles/*.html
@@ -19,23 +24,26 @@ cran:
 test:
 	R -e 'devtools::test()'
 
-README.md: README.Rmd
+README.md: README.Rmd $(articles)
 	# R -e 'devtools::install_deps(".", TRUE)'
 	R -e 'rmarkdown::render("README.Rmd", "all")'
 
-index.md: index.Rmd
+index.md: index.Rmd $(articles)
 	R -e 'rmarkdown::render("index.Rmd", "md_document")'
 
-vignettes/articles/examples.html: vignettes/articles/examples.Rmd vignettes/articles/custom.css
-	R -e 'devtools::build_rmd("vignettes/articles/examples.Rmd")'
+vignettes/articles/%.html: vignettes/articles/%.Rmd $(css)
+	R -e 'devtools::build_rmd("$<")'
+
+# vignettes/articles/examples.html: vignettes/articles/examples.Rmd vignettes/articles/custom.css
+# 	R -e 'devtools::build_rmd("vignettes/articles/examples.Rmd")'
 
-vignettes/articles/visualize-hla-structure.html: vignettes/articles/visualize-hla-structure.Rmd
-	R -e 'devtools::build_rmd("vignettes/articles/visualize-hla-structure.Rmd")'
+# vignettes/articles/visualize-hla-structure.html: vignettes/articles/visualize-hla-structure.Rmd
+# 	R -e 'devtools::build_rmd("vignettes/articles/visualize-hla-structure.Rmd")'
 
-vignettes/articles/numbering.html: vignettes/articles/numbering.Rmd
-	R -e 'devtools::build_rmd("vignettes/articles/numbering.Rmd")'
+# vignettes/articles/numbering.html: vignettes/articles/numbering.Rmd
+# 	R -e 'devtools::build_rmd("vignettes/articles/numbering.Rmd")'
 
-docs/index.html: vignettes/articles/examples.html index.md man/*.Rd
+docs/index.html: index.md $(mans)
 	rm -rf docs/
 	R -e 'pkgdown::init_site(); pkgdown::build_articles(); pkgdown::build_site()'
 	rm -f docs/paper.*

index.Rmd

@@ -41,7 +41,7 @@ See the [usage examples](articles/examples.html) to get some ideas for how to us
 
 - [Logistic regression association for amino acid positions](articles/examples.html#logistic-regression-association-for-amino-acid-positions)
 
-- [UMAP embedding of 3,516 HLA-DRB1 alleles](articles/examples.html#umap-embedding-of-3516-hla-drb1-alleles)
+- [UMAP embedding of 3,671 HLA-DRB1 alleles](articles/examples.html#umap-embedding-of-hla-drb1-alleles)
 
 - [Get HLA allele frequencies from Allele Frequency Net Database (AFND)](articles/examples.html#get-hla-allele-frequencies-from-allele-frequency-net-database-afnd)
 
@@ -54,7 +54,7 @@ See the [usage examples](articles/examples.html) to get some ideas for how to us
 <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="https://slowkow.github.io/hlabud/articles/examples.html#umap-embedding-of-3516-hla-drb1-alleles">
+<a href="https://slowkow.github.io/hlabud/articles/examples.html#umap-embedding-of-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">

index.md

@@ -44,8 +44,8 @@ how to use hlabud in your analyses.
 -   [Logistic regression association for amino acid
     positions](articles/examples.html#logistic-regression-association-for-amino-acid-positions)
 
--   [UMAP embedding of 3,516 HLA-DRB1
-    alleles](articles/examples.html#umap-embedding-of-3516-hla-drb1-alleles)
+-   [UMAP embedding of 3,671 HLA-DRB1
+    alleles](articles/examples.html#umap-embedding-of-hla-drb1-alleles)
 
 -   [Get HLA allele frequencies from Allele Frequency Net Database
     (AFND)](articles/examples.html#get-hla-allele-frequencies-from-allele-frequency-net-database-afnd)
@@ -62,7 +62,7 @@ how to use hlabud in your analyses.
 <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="https://slowkow.github.io/hlabud/articles/examples.html#umap-embedding-of-3516-hla-drb1-alleles">
+<a href="https://slowkow.github.io/hlabud/articles/examples.html#umap-embedding-of-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">

vignettes/articles/numbering.Rmd

@@ -172,7 +172,7 @@ Then, as we move on to `TERVR.LLER`, we add 10 to 11 to get 21 for the `T` amino
 However, as we move on to `CIYNQEE.SV` the rule of "add 10" does not work.
 Instead of labeling `C` as position 31, we label it position 30. Why?
 
-The reason why `C` is 31, and not 30, is because there is an indel (or gap) in the reference sequence at position 25_26 (notice the `.` in `R.L`).
+The reason why `C` is 30, and not 31, is because there is an indel (or gap) in the reference sequence at position 25_26 (notice the `.` in `R.L`).
 The convention is that deletions in the reference sequence are not numbered.
 
 Let's take a closer look at this data with hlabud.
@@ -193,6 +193,7 @@ colnames(a$alleles)[50:70]
 ```
 
 If hlabud is using the correct numbering, then we should see:
+
 - `T` at position 21
 - `C` at position 30