transPlotR
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junjunlab
关于trackVis的问题
我在使用trackVis遇到了一定的问题，我的代码如下：
file <- list.files(pattern = '.bw') data <- loadBigWig(file) save(data,file = 'Data.rda') load('Data.rda') mybw <- data trackVis(bWData = mybw,chr = "Wnk4",region.min = 101167654,region.max = 101168235) 错误信息如下所示： Error in
combine_vars(): ! Faceting variables must have at least one value Runrlang::last_error()to see where the error occurred. Warning messages: 1: In min(x) : no non-missing arguments to min; returning Inf 2: In max(x) : no non-missing arguments to max; returning -Inf 详细展开错误信息如下： <error/rlang_error> Error incombine_vars(): ! Faceting variables must have at least one value
Backtrace: ▆
- ├─base (local)
<fn>(x) - └─ggplot2:::print.ggplot(x)
- ├─ggplot2::ggplot_build(x)
- └─ggplot2:::ggplot_build.ggplot(x)
-
└─layout$setup(data, plot$data, plot$plot_env) -
└─ggplot2 (local) f(..., self = self) -
└─self$facet$compute_layout(data, self$facet_params) -
└─ggplot2 (local) f(...) -
├─ggplot2:::unrowname(...) -
│ └─base::is.data.frame(x) -
└─**ggplot2::combine_vars(data, params$plot_env, vars, drop = params$drop)** -
└─rlang::abort("Faceting variables must have at least one value")
粗体部分似乎为主要问题，期待您的回复
我也遇到了同样的问题。
trackVis(bWData = mybw, gtf.file = gtf.v39, gene.name = 'TP53')
Warning: no non-missing arguments to min; returning InfWarning: no non-missing arguments to max; returning -InfError in combine_vars():
! Faceting variables must have at least one value
Backtrace:
1. base (local) (x)
2. ggplot2:::print.ggplot(x)
4. ggplot2:::ggplot_build.ggplot(x)
5. layout$setup(data, plot$data, plot$plot_env)
6. ggplot2 (local) f(..., self = self)
7. self$facet$compute_layout(data, self$facet_params)
8. ggplot2 (local) f(...)
11. ggplot2::combine_vars(data, params$plot_env, vars, drop = params$drop)
感觉是在寻找gene的时候有问题。用refseq的gtf作为注释文件，画transcript没问题，但是用trackVis会有colname找不到的问题，函数应该是找gene_name，但是refseq默认该列为gene_id
你可以尝试给自己的导入的gtf添加一列gene_name就行了
我加了，但是画track的时候，输入基因名是不对的，显示如上我说的报错。谢谢回复