NAME

App::Plotr - Miscellaneous plots via R

SYNOPSIS

plotr <command> [-?h] [long options...]
        --help (or -h)  show help
                        aka -?

Available commands:

  commands: list the application's commands
      help: display a command's help screen

      hist: histogram
     lines: scatter lines
      tree: draw newick trees
       tsv: convert tsv to xlsx
      venn: Venn diagram
      xlsx: convert xlsx to tsv

Run plotr help command-name for usage information.

DESCRIPTION

App::Plotr draws miscellaneous plots via R

INSTALLATION

# Install Perl and R

# R packages
parallel -j 1 -k --line-buffer '
    Rscript -e '\'' if (!requireNamespace("{}", quietly = TRUE)) { install.packages("{}", repos="https://mirrors.tuna.tsinghua.edu.cn/CRAN") } '\''
    ' ::: \
        extrafont remotes \
        VennDiagram ggplot2 scales gridExtra \
        readr ape

# The Arial font under Ubuntu
sudo apt install ttf-mscorefonts-installer
sudo fc-cache -fv

# System fonts for R
Rscript -e 'library(remotes); options(repos = c(CRAN = "https://mirrors.tuna.tsinghua.edu.cn/CRAN")); remotes::install_version("Rttf2pt1", version = "1.3.8")'
Rscript -e 'library(extrafont); font_import(prompt = FALSE); fonts();'

# This module
cpanm --installdeps https://github.com/wang-q/App-Plotr/archive/0.0.1.tar.gz
curl -fsSL https://raw.githubusercontent.com/wang-q/App-Plotr/master/share/check_dep.sh | bash

cpanm -nq https://github.com/wang-q/App-Plotr.git

EXAMPLES

Example plotr venn

plotr venn t/rocauc.result.tsv t/mcox.05.result.tsv t/mcox.result.tsv --device png -o example/venn.png

Example plotr tree

plotr tree t/YDL184C.nwk --device png -o example/tree.png

Example plotr lines

plotr lines t/d1.tsv \
    --font Helvetica \
    --xl "Distance to indels ({italic(d)[1]})" \
    --yl "Nucleotide divergence ({italic(D)})" \
    --device png -o example/lines.png

Example plotr hist

plotr hist t/hist.tsv \
    -g 2 \
    --width 2 \
    --xl "Weight ({bold(M/F)})" \
    --ymm 0,45 \
    --device png -o example/hist.png

Example plotr tsv

plotr tsv t/rocauc.result.tsv \
    --header \
    --le 4:0.5 --ge 4:0.6 --bt 4:0.52:0.58 --contain 1:m03 \
    -o example/tsv.xlsx

AUTHOR

Qiang Wang wang-q@outlook.com

LICENSE

This software is copyright (c) 2020 by Qiang Wang.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.