microbiomeViz--人生第一个R包

安装

devtools::install_github("lch14forever/microbiomeViz", dependencies = T)

## Skipping install of 'microbiomeViz' from a github remote, the SHA1 (3db1d3a6) has not changed since last install.
##   Use `force = TRUE` to force installation

使用

目前有三个函数：

• parseMetaphlanTSV: 将MetaPhlAn的表格转换成tree格式
• tree.backbone: 做出树的骨架
• clade.anno: 高亮一个节点及其下属所有节点

这个其实是基于之前做桑基图时写的那些代码，将MetaPhlan表格转化为了phylobase的phylo4d类：

library(microbiomeViz)

## Warning: replacing previous import 'ape::rotate' by 'ggtree::rotate' when
## loading 'microbiomeViz'

data("SRS014459_Stool_profile")                    ## 上面的示例数据已经加如microbiomeViz
tr <- parseMetaphlanTSV(SRS014459_Stool_profile)   ## parsing

## Warning: `select_()` is deprecated as of dplyr 0.7.0.
## Please use `select()` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.

## Warning: `as_data_frame()` is deprecated as of tibble 2.0.0.
## Please use `as_tibble()` instead.
## The signature and semantics have changed, see `?as_tibble`.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.

基于ggtree的大戏

做出树的骨架

p <- tree.backbone(tr)

## Warning: `data_frame()` is deprecated as of tibble 1.1.0.
## Please use `tibble()` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.

## Warning: `mutate_()` is deprecated as of dplyr 0.7.0.
## Please use `mutate()` instead.
## See vignette('programming') for more help
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.

p

微生物组常见的操作就是组间比较，我们可以向GraPhlAn那样把显著的节点高亮出来：

## 假设以下taxa在疾病组显著
anno.data <- data.frame(node=c("g__Roseburia", "c__Clostridia", "s__Bacteroides_ovatus"),
                       color='red', stringsAsFactors = FALSE)
p <- clade.anno(p, anno.data)
p

## Warning in max(sp.df$x, na.rm = TRUE): no non-missing arguments to max;
## returning -Inf

## Warning in min(y): no non-missing arguments to min; returning Inf

## Warning in max(y): no non-missing arguments to max; returning -Inf

## Warning in max(sp.df$x, na.rm = TRUE): no non-missing arguments to max;
## returning -Inf

## Warning in min(y): no non-missing arguments to min; returning Inf

## Warning in max(y): no non-missing arguments to max; returning -Inf

## Warning in max(sp.df$x, na.rm = TRUE): no non-missing arguments to max;
## returning -Inf

## Warning in min(y): no non-missing arguments to min; returning Inf

## Warning in max(y): no non-missing arguments to max; returning -Inf

## Warning in max(sp.df$x, na.rm = TRUE): no non-missing arguments to max;
## returning -Inf

## Warning in min(y): no non-missing arguments to min; returning Inf

## Warning in max(y): no non-missing arguments to max; returning -Inf