使用说明：

$ Rscript $scriptdir/ppi_network.r -h
usage: /work/my_stad_immu/scripts/ppi_network.r [-h] -g gene.list [-s ann.db]
                                                [-t score_threshold]
                                                [-v version] [-p prefix]
                                                [-o outdir] [-H height]
                                                [-W width]
GO enrich analysis
optional arguments:
  -h, --help            show this help message and exit
  -g gene.list, --gene.list gene.list
                        diff expressed gene list file, required
  -s ann.db, --species ann.db
                        NCBI taxonomy identifiers of the organism (e.g. 9606
                        for Human, 10090 for mouse). default 9606
  -t score_threshold, --score_threshold score_threshold
                        a threshold for the combined scores of the
                        interactions, such that any interaction below that
                        threshold is not loaded in the network (by default the
                        score threshold is set to 700)
  -v version, --version version
                        define the STRING version to be used [optional,
                        default: 11 ]
  -p prefix, --prefix prefix
                        the output file prefix [optional, default: PPI ]
  -o outdir, --outdir outdir
                        output file directory [default cwd]
  -H height, --height height
                        the height of pic inches [default 10]
  -W width, --width width
                        the width of pic inches [default 10]

参数说明：

-g 指定基因列表文件为SYMBOL ID ：读取文件的第一列为ID列表：STRING数据库获取网络；

使用举例：

Rscript $scriptdir/ppi_network.r -g ../04.deg/S1_vs_S2.DEG.final.tsv -p S1_vs_S2

结果展示：

参考文献：

Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork, Lars J Jensen, Christian von Mering, STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D607–D613, https://doi.org/10.1093/nar/gky1131