index.Rmd

---
title: "Guangchuang Yu's CV"
author: Guangchuang Yu
date: "`r Sys.Date()`"
output:
  pagedown::html_resume:
    css: ['styles.css']
    # set it to true for a self-contained HTML page but it'll take longer to render
    self_contained: true
---

```{r, include=FALSE}
knitr::opts_chunk$set(
  results='asis', 
  echo = FALSE
)


CRANpkg <- function (pkg) {
    cran <- "https://CRAN.R-project.org/package"
    fmt <- "[%s](%s=%s)"
    sprintf(fmt, pkg, cran, pkg)
}

Biocpkg <- function (pkg) {
    sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)
}

library(glue)
library(tidyverse)

# Set this to true to have links turned into footnotes at the end of the document
PDF_EXPORT <- FALSE

# Holds all the links that were inserted for placement at the end
links <- c()

find_link <- regex("
  \\[   # Grab opening square bracket
  .+?   # Find smallest internal text as possible
  \\]   # Closing square bracket
  \\(   # Opening parenthesis
  .+?   # Link text, again as small as possible
  \\)   # Closing parenthesis
  ",
  comments = TRUE)

sanitize_links <- function(text){
  if(PDF_EXPORT){
    str_extract_all(text, find_link) %>% 
      pluck(1) %>% 
      walk(function(link_from_text){
        title <- link_from_text %>% str_extract('\\[.+\\]') %>% str_remove_all('\\[|\\]') 
        link <- link_from_text %>% str_extract('\\(.+\\)') %>% str_remove_all('\\(|\\)')
        
        # add link to links array
        links <<- c(links, link)
        
        # Build replacement text
        new_text <- glue('{title}<sup>{length(links)}</sup>')
        
        # Replace text
        text <<- text %>% str_replace(fixed(link_from_text), new_text)
      })
  }
  
  text
}


cp2012 <- function() {
  cat("\n\n::: aside\n\n")
  cat("![](figures/2021年中国科技论文统计报告发布会-高被引论文-截屏.png){width=100%}\n\n")
  clusterProfiler <- "clusterProfiler (Yu et al. 2012)"
  url <- "https://doi.org/10.1089/omi.2011.0118"
  clusterProfiler2012 <- glue("[{clusterProfiler}]({url})")

  glue(
    "{clusterProfiler2012} 被中国科学技术信息研究所列为“2011-2021我国高被引论文中被引次数最高的10篇国际论文”（2021年中国科技论文统计报告）" 
  ) %>% print()

  cat("\n\n:::\n\n")
}


cp2021 <- function() {
  cat("\n\n::: aside\n\n")
  cat("![](figures/cell+press-screenshot-2021-08-24.jpg){width=100%}\n\n")

  clusterProfiler4 <- "clusterProfiler (Wu et al. 2021)"
  url <- "https://doi.org/10.1016/j.xinn.2021.100141"
  clusterProfiler2021 <- glue("[{clusterProfiler4}]({url})")

  glue(
    "{clusterProfiler2021}, the featured article in 2021-08-24's website banner of Cell Press" 
  ) %>% print()

  cat("\n\n:::\n\n")
}



ggtree2017 <- function() {
  cat("\n\n::: aside\n\n")
  cat("![](figures/10th-anniversary-logo-2.png){width=100%}\n\n")

  # ggtree <- "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data"
  ggtree <- "ggtree (Yu et al. 2017)"
  url <- 'http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract'

  ggtree2 <- glue("[{ggtree}]({url})")
  journal <- "**_Methods in Ecology and Evolution_**"

  url2 <- "https://methodsblog.com/2020/11/19/ggtree-tree-visualization/"
  journal2 <- glue("[{journal}]({url2})")

  glue(
    " 
    The {ggtree2} paper was selected as a feature article to celebrate the 10^th^ anniversary of the launch of {journal2}.
    "
  ) %>% print()

  cat("\n\n:::\n\n")
}



# Takes a single row of dataframe corresponding to a position
# turns it into markdown, and prints the result to console.
build_position_from_df <- function(pos_df){
  

  if (grepl("clusterProfiler", pos_df$title) && grepl("OMICS", pos_df$loc)) {
    cp2012()
  }


  if (grepl("clusterProfiler 4.0", pos_df$title) && grepl("Innovation", pos_df$loc)) {
    cp2021()
  }


  missing_start <- pos_df$start == 'N/A'
  dates_same <- pos_df$end == pos_df$start
  if (pos_df$end == 9999) {
    pos_df$end = "present"
  }
  if(any(c(missing_start,dates_same))){
    timeline <- pos_df$end
  } else {
    timeline <- glue('{pos_df$end} - {pos_df$start}')
  }

  descriptions <- pos_df[str_detect(names(pos_df), 'description')] %>% 
    as.list() %>% 
    map_chr(sanitize_links)
  
  # Make sure we only keep filled in descriptions
  description_bullets <- paste('-', descriptions[descriptions != 'N/A'], collapse = '\n')
  
  if (length(description_bullets) == 1 && description_bullets == "- ") {
    description_bullets <- ""
  }
  glue(
"### {sanitize_links(pos_df$title)}

{pos_df$loc}

{pos_df$institution}

{timeline}

{description_bullets}


"
  ) %>% print()


  if (grepl("ggtree", pos_df$title) && grepl("Ecology and Evolution", pos_df$loc)) {
    ggtree2017()
  }




}

# Takes nested position data and a given section id 
# and prints all the positions in that section to console
print_section <- function(position_data, section_id){
  x <- position_data %>% 
    filter(section == section_id) %>% 
    pull(data) 
  
  prese <- " - "
  xx <- list()

  for (i in seq_along(x)) {    
      y = x[[i]]
      y <- cbind(y, start2 = as.character(y$start))
      y <- cbind(y, end2 = as.character(y$end))

      se <- paste(y$start, "-", y$end, collapse = " ")
      if (prese == se) {
        y$start2 = ""
        y$end2 = ""
      } else {
        prese = se
      }

    xx[[i]] <- select(y, -c(start, end)) %>%
      rename(start=start2, end=end2)
  }
    
  xx %>% 
    purrr::walk(build_position_from_df)
}



fill_nas <- function(column){
  ifelse(is.na(column), 'N/A', column)
}

# Load csv with position info
position_data <- read_csv('positions.csv') %>% 
  mutate_all(fill_nas) %>% 
  arrange(order, desc(end)) %>% 
  mutate(id = 1:n()) %>% 
  nest(data = c(-id, -section))
```

```{r}
# When in export mode the little dots are unaligned, so fix that. 
if(PDF_EXPORT){
  cat("
  <style>
  :root{
    --decorator-outer-offset-left: -6.5px;
  }
  </style>")
}
```

Aside
================================================================================


![logo](ygc-2024.jpg){width=100%}

```{r}
# When in export mode the little dots are unaligned, so fix that. 
if(PDF_EXPORT){
  cat("View this CV online with links at _guangchuangyu.github.io/cv_")
}
```

Contact {#contact}
--------------------------------------------------------------------------------


- <i class="fa fa-envelope"></i> gcyu1@smu.edu.cn
- <i class="fa fa-twitter"></i> guangchuangyu
- <i class="fa fa-github"></i> github.com/YuLab-SMU
- <i class="fa fa-link"></i> https://yulab-smu.top/
- <i class="fa fa-weixin"></i> YuLabSMU (公众号)
- <i class="fa fa-phone"></i> +86-20-61648632

<br>

```{r}
profile = jsonlite::fromJSON("profile.json")
cites = jsonlite::fromJSON("citation.json")
if (profile$total_cites < sum(cites$cites))
  profile$total_cites <- sum(cites$cites)

hcr_symbol = '<font color="#cc5500"><i class="fa fa-trophy"></i></font>'

glue(

"
+ {hcr_symbol} Highly Cited Researcher
+ Citation = {profile$total_cites}
+ H-index = {profile$h_index}
+ I10-index = {profile$i10_index}

"
  ) %>% print()

```

![](citation.png)




Disclaimer {#disclaimer}
--------------------------------------------------------------------------------


Last updated on `r Sys.Date()`.



Main
================================================================================

Guangchuang Yu {#title}
--------------------------------------------------------------------------------


```{r, results='asis'}
#intro_text <- glue("Professor of Bioinformatics at [Southern Medical University](http://www.smu.edu.cn/). I have developed more than 20 R packages, including ",
#  {Biocpkg("clusterProfiler")}, ", ", 
#  {Biocpkg("ChIPseeker")}, ", ",
#  {Biocpkg("treeio")}, " and ",
#  {Biocpkg("ggtree")}, 
#  ", to help biologists to explore and understand their data.")

#cat(sanitize_links(intro_text))
```

<!-- I am broadly interested in bioinformatics, metagenomics, molecular evolution, data integration and visualization. -->

Professor and dean of the Department of Bioinformatics, School of Basic Medicine, Southern Medical University. 

My research group is dedicated to developing innovative methods, tools, and novel analytical approaches through multidisciplinary integration to address complex problems in the field of biomedicine.

教授、博导，现任南方医科大学基础医学院生物信息学系系主任。

课题组致力于通过多学科交叉融合，开发创新方法、工具以及新颖的分析手段，以解决生物医学领域复杂问题。 


Research Experience {data-icon=laptop}
--------------------------------------------------------------------------------

```{r, results='asis', echo = FALSE}
print_section(position_data, 'research_positions')
```


Education {data-icon=graduation-cap data-concise=true}
--------------------------------------------------------------------------------

```{r, results='asis', echo = FALSE}
print_section(position_data, 'education')
```



Certificate {data-icon=book}
--------------------------------------------------------------------------------



```{r, results='asis', echo = FALSE}
print_section(position_data, 'certificate')
```


Scholarships & Awards {data-icon=trophy}
--------------------------------------------------------------------------------

::: aside
![](figures/HCR2024.png){width=100%}
![](figures/HCR2023.png){width=100%}
![](figures/top-2-percent-scientist-2024.png){width=100%}
:::


```{r}
print_section(position_data, 'award')
```



Grants  {data-icon=chart-line}
--------------------------------------------------------------------------------

::: aside
![](figures/9781032233574_cover_review.png){width=100%}

![](figures/book-cover-cn.png){width=100%}
:::


```{r}
print_section(position_data, 'grant')
```


Books {data-icon=book}
--------------------------------------------------------------------------------



```{r}
print_section(position_data, 'book_chapters')
```


Teaching Experience {data-icon=chalkboard-teacher}
--------------------------------------------------------------------------------

```{r}
print_section(position_data, 'teaching_positions')
```

<div style="page-break-after: always; visibility: hidden"> 
<!--  
\pagebreak 
-->
</div>




Publications {data-icon=book}
--------------------------------------------------------------------------------


```{r}
print_section(position_data, 'academic_articles')
```



Conference proceedings {data-icon=group}
--------------------------------------------------------------------------------



```{r}
print_section(position_data, 'presentation')
```


Professional affliations {data-icon=home}
--------------------------------------------------------------------------------



```{r}
print_section(position_data, 'affliation')
```


```{r}
if(PDF_EXPORT){
  cat("
  
Links {data-icon=link}
--------------------------------------------------------------------------------



")
  
  walk2(links, 1:length(links), function(link, index){
    print(glue('{index}. {link}'))
  })
}
```