R语言的tsne_analysis.r怎么使用

本篇内容主要讲解"R语言的tsne_analysis.r怎么使用"，感兴趣的朋友不妨来看看。本文介绍的方法操作简单快捷，实用性强。下面就让小编来带大家学习"R语言的tsne_analysis.r怎么使用"吧!

tsne_analysis.r 表达聚类分析

使用说明：

$ Rscript $scriptdir/tsne_analysis.r -husage: /work/my_stad_immu/scripts/tsne_analysis.r [-h] -i filepath -m metadata                                                  [-d dims] [-p perplexity]                                                  [--theta theta]                                                  [-M initial_dims] [-T top]                                                  -g group [-s size]                                                  [-a alpha] [-e] [-L]                                                  [-X x.lab] [-Y y.lab]                                                  [-t title] [-o outdir]                                                  [-n prefix] [-H height]                                                  [-W width]t-Distributed Stochastic Neighbor Embedding t-SNE analysis:https://www..com/article/1498optional arguments:  -h, --help            show this help message and exit  -i filepath, --input filepath                        input the dataset martix [required]  -m metadata, --metadata metadata                        input metadata file path[required]  -d dims, --dims dims  set Output dimensionality [default=2]  -p perplexity, --perplexity perplexity                        Perplexity parameter (should not be bigger than 3 *                        perplexity < nrow(X) - 1, see details for                        interpretation) [default 50]  --theta theta         Speed/accuracy trade-off (increase for less accuracy),                        set to 0.0 for exact TSNE [default 0.5]  -M initial_dims, --initial_dims initial_dims                        the number of dimensions that should be retained in                        the initial PCA step [default 50]  -T top, --top top     select top gene to analysis [default NULL]  -g group, --group group                        input group id in metadata file to fill                        color[required]  -s size, --size size  point size [optional, default: 3]  -a alpha, --alpha alpha                        point transparency [0-1] [optional, default: 1]  -e, --ellipse         whether draw ellipse [optional, default: False]  -L, --label           whether show pionts sample name [optional, default:                        False]  -X x.lab, --x.lab x.lab                        the label for x axis [optional, default: t-SNE1]  -Y y.lab, --y.lab y.lab                        the label for y axis [optional, default: t-SNE2]  -t title, --title title                        the label for main title [optional, default: t-SNE]  -o outdir, --outdir outdir                        output file directory [default cwd]  -n prefix, --name prefix                        out file name prefix [default demo]  -H height, --height height                        the height of pic inches [default 5]  -W width, --width width                        the width of pic inches [default 5]

参数说明

使用举例：

#降维验证分组#####t-SNERscript $scriptdir/tsne_analysis.r -i immu/ssgsea.res.tsv -m metadata.group.tsv \  -o tsne -g subtype.hclust -p 6 -n tsne

到此，相信大家对"R语言的tsne_analysis.r怎么使用"有了更深的了解，不妨来实际操作一番吧！这里是网站，更多相关内容可以进入相关频道进行查询，关注我们，继续学习！