exp_immu_cor_plot.r 基因表达量与免疫侵润相关性绘图分析

exp_immu_cor_plot.r 基因表达量与免疫侵润相关性绘图分析

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


ID TCGA-D7-A74A-01A-11R-A32D-31 TCGA-BR-7704-01A-11R-2055-13 TCGA-VQ-A91N-01A-11R-A414-31 TCGA-CD-A4MH-01A-11R-A251-31
NUP50 18.65505 31.59232 28.23382 28.76485
CXCR4 64.85805 125.123 56.35244 69.98976
NT5E 111.4818 69.8587 79.37382 25.05824
EFNA3 8.247857 42.03308 43.46432 26.66024
STC1 4.781111 21.36327 40.81077 19.51568
ZBTB7A 95.51678 103.4768 158.3024 126.2677
CLDN9 1.187456 2.476138 0.366081 7.347344


-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


cell_type TCGA-B7-A5TK-01A-12R-A36D-31 TCGA-BR-7959-01A-11R-2343-13 TCGA-IN-8462-01A-11R-2343-13 TCGA-BR-A4CR-01A-11R-A24K-31
B cell 0 0.013159742 0.000907507 0.020234
T cell CD4+ 0 0.114882797 0.118061151 0.152274
T cell CD8+ 0.771121767 0.130798349 0.048964712 0.005392
Neutrophil 0.22692792 0.125194736 0.106562343 0.057013
Macrophage 0 0.213365358 0 0.05444
Myeloid dendritic cell 0.935644191 0.457844399 0.404774813 0.296719



绘图输出结果:




attachments-2021-06-H97WOu1S60c849c0bfd25.png


  • 发表于 2021-06-15 14:33
  • 阅读 ( 2499 )
  • 分类:TCGA

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