diff --git a/Makefile b/Makefile index 8b07944..71298a7 100644 --- a/Makefile +++ b/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.* diff --git a/index.Rmd b/index.Rmd index f109c3a..ccdab4a 100644 --- a/index.Rmd +++ b/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 - + diff --git a/index.md b/index.md index 96bb614..41c36fa 100644 --- a/index.md +++ b/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. - + diff --git a/vignettes/articles/examples_files/figure-html/umap-2digit-1.png b/vignettes/articles/examples_files/figure-html/umap-2digit-1.png index 09fc57f..bdafc21 100644 Binary files a/vignettes/articles/examples_files/figure-html/umap-2digit-1.png and b/vignettes/articles/examples_files/figure-html/umap-2digit-1.png differ diff --git a/vignettes/articles/examples_files/figure-html/umap-57-1.png b/vignettes/articles/examples_files/figure-html/umap-57-1.png index 3160652..edbc699 100644 Binary files a/vignettes/articles/examples_files/figure-html/umap-57-1.png and b/vignettes/articles/examples_files/figure-html/umap-57-1.png differ diff --git a/vignettes/articles/examples_files/figure-html/umap-D57-1.png b/vignettes/articles/examples_files/figure-html/umap-D57-1.png index 8cb419a..5253e29 100644 Binary files a/vignettes/articles/examples_files/figure-html/umap-D57-1.png and b/vignettes/articles/examples_files/figure-html/umap-D57-1.png differ diff --git a/vignettes/articles/numbering.Rmd b/vignettes/articles/numbering.Rmd index c15867e..0439be4 100644 --- a/vignettes/articles/numbering.Rmd +++ b/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