R语言的hclust_analysis.r如何使用

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hclust_analysis.r 转录组数据层次聚类分析

使用说明：

usage: hclust_analysis.r [-h] -i filepath [-d distance] [-m method] [-T top]                         [-S] [-M max.nc] [-k bestk] [-s size] [-a alpha] [-e]                         [-L] [-X label] [-Y label] [-t label] [-o path]                         [-H number] [-W number]Hierarchical Clustering andplot：https://clincancerres.aacrjournals.org/content/25/16/5002optional arguments:  -h, --help            show this help message and exit  -i filepath, --input filepath                        input the dataset martix [required]  -d distance, --distance distance                        the distance measure to be used to compute the                        dissimilarity matrix. This must be one of:                        "euclidean", "maximum", "manhattan", "canberra",                        "binary", "minkowski" . By default,                        distance="euclidean".  -m method, --method method                        the cluster analysis method to be used. This should be                        one of: "ward.D", "ward.D2", "single", "complete",                        "average", "mcquitty", "median", "centroid". by                        default method=ward.D  -T top, --top top     select top gene to analysis [default NULL]  -S, --scale           scale data sd=1 mean=0 [default FALSE]  -M max.nc, --max.nc max.nc                        maximal number of clusters for nbclust, between 2 and                        (number of objects - 1), greater or equal to min.nc.                        By default [optional, default: 15]  -k bestk, --bestk bestk                        set bestk or nbclust choose bestk [optional, default:                        NULL]  -X label, --x.lab label                        the label for x axis [optional, default: sample ]  -Y label, --y.lab label                        the label for y axis [optional, default: Distance ]  -t label, --title label                        the label for main title [optional, default: Cluster                        Dendrogram]  -o path, --outdir path                        output file directory [default cwd]  -H number, --height number                        the height of pic inches [default 5]  -W number, --width number                        the width of pic inches [default 10]

使用方法：

应该运行两次

#第一次运行不指定K，通过nbclust 结果选择合适的K （亚型）Rscript $scriptdir/hclust_analysis.r -i immu/ssgsea.res.tsv  -o hclust  -M 20 --distance "euclidean"  #再次运行指定最佳K，输出聚类树和分组表格Rscript $scriptdir/hclust_analysis.r -i immu/ssgsea.res.tsv  -o hclust   --distance "euclidean" -k 2

参数说明：

-i 输入基因表达矩阵文件，或者免疫侵润矩阵文件

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