publications.Rmd

---
# Publications widget.
# This widget displays recent publications from `content/publication/`.

date: "2025-01-01T00:00:00"
draft: false

title: "Publications"
subtitle: ""
widget: "custom_vertical"

# Order that this section will appear in.
weight: 3

# Number of publications to list.
count: 10

# Show publication details (such as abstract)? (true/false)
detailed_list: false

---

```{r, include=FALSE}
knitr::opts_chunk$set(echo=FALSE, message=FALSE, warning=FALSE)
```


```{r readbib}
library(RefManageR)
library(magrittr)
library(dplyr)

bib <- ReadBib('../../misc/HS-publication.bib')

convertBold <- function(cc){
  sapply(cc, function(ccc){
    if(grepl('\\\\bf', ccc)){
      ccc %>% gsub('\\\\bf', '', .) %>% paste0('<strong>', ., '</strong>') %>% return
    } else {
      return(ccc)
    }
  })
}
convertStars <- function(cc){
  cc %>% gsub('\\*', '\\\\*', .)
}

bib.df <- lapply(bib, function(bibi) {
  data.frame(
    title = if (!is.null(bibi$title)) gsub('\\{', '', gsub('\\}', '', bibi$title)) else NA,
    year = if (!is.null(bibi$year)) as.numeric(bibi$year) else NA,
    doi = if (!is.null(bibi$doi)) bibi$doi else NA,
    journal = if (!is.null(bibi$journal)) {
      gsub('.*\\}\\{(.*)\\}', '\\1', bibi$journal)
    } else if (!is.null(bibi$booktitle)) {
      gsub('.*\\}\\{(.*)\\}', '\\1', bibi$booktitle)
    } else {
      NA
    },
    author = if (!is.null(bibi$author)) {
      bibi$author %>%
        as.character() %>%
        convertBold %>%
        convertStars %>%
        paste(collapse = ', ')
    } else {
      NA
    },
    keywords = if (!is.null(bibi$keywords)) bibi$keywords else '',
    pmid = if (!is.null(bibi$pmid)) bibi$pmid else '',
    preprintdoi = if (!is.null(bibi$preprintdoi)) bibi$preprintdoi else '',
    scripts = if (!is.null(bibi$scripts)) bibi$scripts else '',
    press = if (!is.null(bibi$pressurl)) bibi$pressurl else '',
    stringsAsFactors = FALSE
  )
})

bib.df = do.call(rbind, bib.df)
bib.df %<>% mutate(rk=1:n())

```

```{r outlist, results='asis'}
htmlCit <- function(df){
  ## Button linking to PubMed Central
  pmcid = ''
  if(df$pmid != ''){
    pmcid = paste0(' <a class="btn btn-primary btn-outline btn-xs" target=\"_blank\" href="https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/', df$pmid, '">PubMed Central</a>')
  }
  ## Button linking to the preprint
  preprintdoi = ''
  if(df$preprintdoi != ''){
    preprintdoi = paste0(' <a class="btn btn-primary btn-outline btn-xs" target=\"_blank\" href="https://doi.org/', df$preprintdoi, '">Preprint</a>')
  }
  ## Button linking to the repo with scripts
  scripts = ''
  if(df$scripts != ''){
    scripts = paste0(' <a class="btn btn-primary btn-outline btn-xs" target=\"_blank\" href="', df$scripts, '">Data/Code</a>')
  }
  ## Button linking to the press page
  press = ''
  if(df$press != ''){
    press = paste0(' <a class="btn btn-primary btn-outline btn-xs" href="/fixed/', df$press, '">Press</a>')
  }
  ## Start a "row"
  cat('<li itemscope itemtype="http://schema.org/CreativeWork"><i class="fa-li fa fa-file-text-o" aria-hidden="true"></i>')
  cat('<div class="row">')
  ## Article info and links
  cat('<div class="col-md-10"><span itemprop="name">', df$title, '. <a target=\"_blank\" href="https://doi.org/',
      df$doi, '">', df$journal, ' ', df$year, '.</a></span><div class="authorpub">', df$author, '</div>', pmcid, preprintdoi, scripts, press, '</div>', sep='')
  ## Badges
  cat('<div class="col-md-2">')
  cat(paste0('<span class="__dimensions_badge_embed__" data-doi="', df$doi, '" data-hide-zero-citations="true" data-style="small_rectangle"></span>'))
  cat(paste0('<div data-badge-type="2" data-doi="',df$doi,'" data-hide-no-mentions="true" data-hide-less-than="1" class="altmetric-embed" data-badge-popover="left" data-link-target="_blank"></div>'))
  if(df$preprintdoi != ''){
    cat(paste0('<span class="__dimensions_badge_embed__" data-doi="', df$preprintdoi, '" data-hide-zero-citations="true" data-style="small_rectangle"></span>'))
    cat(paste0('<div data-badge-type="2" data-doi="',df$preprintdoi,'" data-hide-no-mentions="true" data-hide-less-than="1" class="altmetric-embed" data-badge-popover="left" data-link-target="_blank"></div>'))
  }
  cat('</div>')
  ## End article "row"
  cat('</div>')
  cat('</li>')
  data.frame()
}

cat('<ul class="fa-ul">')
dump = bib.df %>% filter(!grepl('Under review', journal), !grepl('no-website', keywords)) %>% group_by(desc(year),rk,title) %>% do(htmlCit(.))
cat('</ul>')

## cat('<h3>Consortia publications</h3>\n<ul class="fa-ul">')
## dump = bib.df %>% filter(!grepl('Under review', journal), grepl('no-website', keywords)) %>% group_by(desc(year),rk,title) %>% do(htmlCit(.))
## cat('</ul>')

##And here is the [PDF of my PhD thesis](https://github.com/jmonlong/phdthesis/releases/download/final/Monlong_Jean_HumanGenetics_thesis.pdf) on "*Population-Based Approaches to Characterize Copy Number Variation from Whole-Genome Sequencing in Healthy Individuals and ##Disease Cohorts*" ([LaTeX source](https://github.com/jmonlong/phdthesis)).

```