index.Rmd

---
author: '**David Simon Kleinhans**'
date: 'Frankfurt am Main, 2021'
institution: 'Johann Wolfgang Goethe-Universität'
division: 'Entwicklungsbiologie der Vertebraten'
advisor: 'Prof. Dr. Sven Klimpel'
altadvisor: 'Prof. Dr. Virginie Lecaudey'
department: 'Fachbereich Biowissenschaften'
degree: '**PhD in Biology**'
title: '**Genetic and Mechanic Signaling in Organ Development**'
knit: "bookdown::render_book"
site: bookdown::bookdown_site
output: 
  thesisdown::thesis_pdf:
    highlight: monochrome # https://stackoverflow.com/questions/30880200/pandoc-what-are-the-available-syntax-highlighters
    toc_depth: 4
  #thesisdown::thesis_gitbook:
  #  highlight: monochrome # https://stackoverflow.com/questions/30880200/pandoc-what-are-the-available-syntax-highlighters

#  thesisdown::thesis_word: default
#  thesisdown::thesis_epub: default
# If you are creating a PDF you'll need to write your preliminary content here or
# use code similar to line 20 for the files.  If you are producing in a different
# format than PDF, you can delete or ignore lines 20-31 in this YAML header.
#abstract: |
#  `r if(knitr:::is_latex_output()) paste(readLines("00-abstract.Rmd"), collapse = '\n  ')`
# If you'd rather include the preliminary content in files instead of inline
# like below, use a command like that for the abstract above.  Note that a tab is 
# needed on the line after the |.,

bibliography: files/refs/library.bib
csl: files/refs/science.csl
lot: true
lof: true
disclosure: |
  Unless otherwise noted, all figures in this manuscript are an expression of my own creative achievement. Similarities between molecule, protein and signalling models exist and are based on well-known textbooks such as Lodish et al., Molecular Cell Biology, 5th Edt. and Scott F. Gilbert et al., Developmental Biology 11th Edt. 
#space_between_paragraphs: true
#- \usepackage{tikz}
---

```{r include-packages, include = FALSE}
if(!require(devtools))
  install.packages("devtools", repos = "http://cran.rstudio.com")
if(!require(thesisdown))
  devtools::install_github("ismayc/thesisdown")
library(thesisdown)
```

```{r chunkopts, include = FALSE}
# chunks
  knitr::opts_chunk$set(
    out.width = '95%',
    echo = FALSE,
    cache = FALSE,
    warning = FALSE,
    message = FALSE,
    fig.align = 'center', 
    dpi = 200,# fig.pos = 'H',
    dev.args = list(bg = "transparent"), 
    dev = 'png'
    ) #, dev='pdf'
# define options for text size
  def.chunk.hook  <- knitr::knit_hooks$get("chunk")
  knitr::knit_hooks$set(chunk = function(x, options) {
    x <- def.chunk.hook(x, options)
    ifelse(options$size != "normalsize", paste0("\n \\", options$size,"\n\n", x, "\n\n \\normalsize"), x)
  })
# libraries
  library(pROC)
  library(ggplot2)
  library(ggpubr)
  library(pander)
  library(kableExtra)
  library(tidyverse)
# colors
  jet.colors <- 
    colorRampPalette(
      c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000")
      )
  angle.colors <- 
    colorRampPalette(
      c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000", 
        "red", "#FF7F00", "yellow","#7FFF7F", "cyan", "#007FFF", "blue", "#00007F"))
```

```{r table-chunkopts, echo = FALSE}
# latex format if knitr output is latex
if (knitr:::is_latex_output()) {
  options(knitr.table.format = "latex") 
}
# remove NAs
options(knitr.kable.NA = '')
```