使用方法：

$Rscript ../scripts/exp_immu_cor_plot.r -h

usage: ../scripts/exp_immu_cor_plot.r [-h] -e expset -i immu [-m method]
                                      [-a alternative] [-n ncol] [-l]
                                      [-x label.x.npc] [-y label.y.npc]
                                      [-o outdir] [-H height] [-W width]

scattor correlateion plot: https://www.omicsclass.com/article/1488

optional arguments:
  -h, --help            show this help message and exit
  -e expset, --expset expset
                        set event column name [required]
  -i immu, --immu immu  input data file path[required]
  -m method, --method method
                        a character string indicating which correlation
                        coefficient (or covariance) is to be computed. One of
                        "pearson", "kendall", or "spearman". [default pearson]
  -a alternative, --alternative alternative
                        a character string specifying the alternative
                        hypothesis, must be one of "two.sided" , "greater" or
                        "less". You can specify just the initial letter.
                        [default two.sided]
  -n ncol, --ncol ncol  column num [default [default 4]
  -l, --log2            Whether to do log2 transformation of gene expression
                        [default FALSE]
  -x label.x.npc, --label.x.npc label.x.npc
                        value should be between 0 and 1. Coordinates to be
                        used for positioning the label, expressed in
                        "normalized parent coordinates". [default 0]
  -y label.y.npc, --label.y.npc label.y.npc
                        value should be between 0 and 1. Coordinates to be
                        used for positioning the label, expressed in
                        "normalized parent coordinates". [default 1]
  -o outdir, --outdir outdir
                        output file directory [default cwd]
  -H height, --height height
                        the height of pic inches [default 5]
  -W width, --width width
                        the width of pic inches [default 10]

使用举例：

Rscript ../scripts/exp_immu_cor_plot.r  -e gene_exp1.tsv -i ../03.TIME/immu/timer.res.tsv  -o timer_cor1 --log2

参数说明：

-e 指定输入指定基因的表达量,行为 基因，列为样本名称

-i 输入样本免疫侵润结果， 注意脚本会自动对两个文件里的样本取交集

绘图输出结果：