R语言的heatmap_group_plot.r如何使用

本篇内容主要讲解"R语言的heatmap_group_plot.r如何使用"，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heatmap_group_plot.r如何使用"吧!

heatmap_group_plot.r 分组热图展示免疫侵润结果

使用参数说明：

$ Rscript   heatmap_group_plot.r -husage:  heatmap_group_plot.r [-h] -i filepath -m                                                          filepath -g group                                                          [group ...]                                                          [-l filepath]                                                          [-t topnumber]                                                          [--scale SCALE]                                                          [--log2]                                                          [--cluster_rows]                                                          [--cluster_cols]                                                          [--show_rownames]                                                          [--show_colnames]                                                          [-c color [color ...]]                                                          [-o outdir]                                                          [-p prefix]                                                          [-H height]                                                          [-W width]plot heatmapoptional arguments:  -h, --help            show this help message and exit  -i filepath, --input filepath                        input the immune res data,[required]  -m filepath, --metadata filepath                        input metadata file path[required]  -g group [group ...], --group group [group ...]                        input group id in metadata file, can set multi                        groups[required]  -l filepath, --genelist filepath                        gene list file to keep [default NULL]  -t topnumber, --top topnumber                        The top var to plot [default NULL]  --scale SCALE         character indicating if the values should be centered                        and scaled in either the row direction or the column                        direction, or none. Corresponding values are "row",                        "column" and "none" [default="row"]  --log2                whether do log2 transfrom [optional, default: False]  --cluster_rows        whether cluster_rows [optional, default: False]  --cluster_cols        whether cluster_cols [optional, default: False]  --show_rownames       whether show_rownames [optional, default: False]  --show_colnames       whether show_colnames [optional, default: False]  -c color [color ...], --color color [color ...]                        color map of heatmap, give three color                        [default=c('blue', 'white', 'red')  -o outdir, --outdir outdir                        output file directory [default cwd]  -p prefix, --prefix prefix                        out file name prefix [default demo]  -H height, --height height                        the height of pic inches [default 9]  -W width, --width width                        the width of pic inches [default 10]

注意事项：

样本分组 metadata文件中，不要有NA值；不然会报错：

Error in names(ann_colors[[opt$group[i]]]) <- unique(mygroup) :   'names' attribute [12] must be the same length as the vector [11]

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