How to make a box-plot with jittered points for multiple groups

Make a box-plot with jittered points for multiple groups using ggplot2

Let me demonstrate it with an example. Use the ToothGrowth data set in the ggplot2 library

library(ggplot2)

ggplot(ToothGrowth, aes(x=as.factor(dose), y=len, color=supp)) + 
        geom_boxplot(position=position_dodge(0.9))+
        geom_jitter(position=position_dodge(0.9)) +
        xlab("dose")

I want to make the points separate from each other rather than on the same vertical line.

ggplot(ToothGrowth, aes(x= as.factor(dose), y=len, color= supp,fill= supp)) + 
        geom_point(position=position_jitterdodge(dodge.width=0.9)) +
        geom_boxplot(fill="white", alpha=0.1, outlier.colour = NA, 
                     position = position_dodge(width=0.9)) +
        xlab("dose")

convert html to pdf by pandoc

Pandoc is a very useful tool to convert common formats.

First install pandoc on mac by:

brew install pandoc

pandoc requires pdflatex to convert to pdfs.

install mactex:
download it and just double click it should install it.

next, put executables including latexpdf to the path.

echo export PATH=$PATH:/usr/texbin/ >> .bashrc
source ~/.bashrc

You can specify margins of the pdf by -V geometry:margin=1in:

pandoc http://quinlanlab.org/tutorials/cshl2013/gemini.html -V geometry:margin=1in -o gemini.pdf`  

when codes in html are too long, they get cut-off

Very thankful, I found the answer in this post:

Save the following as listings-setup.tex

% Contents of listings-setup.tex
\usepackage{xcolor}

\lstset{
    basicstyle=\ttfamily,
    numbers=left,
    keywordstyle=\color[rgb]{0.13,0.29,0.53}\bfseries,
    stringstyle=\color[rgb]{0.31,0.60,0.02},
    commentstyle=\color[rgb]{0.56,0.35,0.01}\itshape,
    numberstyle=\footnotesize,
    stepnumber=1,
    numbersep=5pt,
    backgroundcolor=\color[RGB]{248,248,248},
    showspaces=false,
    showstringspaces=false,
    showtabs=false,
    tabsize=2,
    captionpos=b,
    breaklines=true,
    breakatwhitespace=true,
    breakautoindent=true,
    escapeinside={\%*}{*)},
    linewidth=\textwidth,
    basewidth=0.5em,
}

Then, invoke pandoc:

pandoc https://cran.r-project.org/web/packages/gapmap/vignettes/tcga_example.html --listings -H listings-setup.tex -o gapmap_TCGA.pdf