使用说明：

$ Rscript $scriptdir/tsne_analysis.r -h
usage: /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.omicsclass.com/article/1498

optional 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-SNE
Rscript $scriptdir/tsne_analysis.r -i immu/ssgsea.res.tsv -m metadata.group.tsv \
  -o tsne -g subtype.hclust -p 6 -n tsne

结果展示：

引用：

Rtsne包  https://github.com/jkrijthe/Rtsne