microbiota / amplicon Goto Github PK

Thanks for all your work sincerely! That's a great achievement and it benefit me most. While when i run the code in R，there are some problem. The data i used to run code is come from yours.

#Warning message:
#Factor Kingdom contains implicit NA, consider using forcats::fct_explicit_na

so, i want to know whether you have time to solve my problem, thanks a lot!

绘图时根据分组在X轴来排列样品，但是有的组中含有的样品较多，有的组较少。这种情况下绘制的图bar的宽度有大有小，导致图片不美观，同时也影响了空间的利用，即样品较多的组中bar非常细，导致看不清楚，而样品较少的组中bar非常宽，占用了很多空间，是否可以进行调整，使得bar的宽度一致，而分组的宽度随着组内样品的多少而自由伸缩？

i first used R3.6.3 to install it, but some errors showed it cant be installed. then i change r4.0.0 to install it, but the same error occured. what version r is suit to install it

Hello, I've tried to use some basic functions provided within microbiota/amplicon, although they seem very interesting current lack of integration reading metadata or otu_table from phyloseq objects or biom itself hampers its usage.

One suggestion, in case the developer does not want to provide this integration, is to provide an example of the input files (i.e. alpha_boxplot tables obtained used usearch).

Best,

错误报告如下：

p = alpha_boxplot(alpha_div, index = shannon, metadata, groupID = "Back")
Error in [.data.frame(alpha_div, rownames(sampFile), index) :
object 'shannon' not found
p = alpha_boxplot(alpha_div, index = richness, metadata, groupID = "Back")
Error in [.data.frame(alpha_div, rownames(sampFile), index) :
object 'richness' not found

另外还有一个问题请教老师，就是原生R语言环境，采用R脚本运行，就是Rscript alpha_boxplot.R时弹出找不到对象p是怎么回事，把那句“p”的判断语句直接注释掉，又报错说找不到make_option函数

> install_local("C://tempscp//amplicon-master.zip")
Installing package into ‘C:/Users/Wolvesled/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package 'amplicon' ...
** using staged installation
** R
Error : (converted from warning) unable to re-encode 'BetaDiv.R' lines 120, 170, 201
ERROR: unable to collate and parse R files for package 'amplicon'
* removing 'C:/Users/Wolvesled/Documents/R/win-library/4.0/amplicon'
Error: Failed to install 'amplicon-master.zip' from local:
  (converted from warning) installation of package ‘C:/Users/******/amplicon-master’ had non-zero exit status

seems encoding error at 'BetaDiv.R' lines 120, 170, 201

Hello!
I am running the code below which do not work. The pyseq and group should be fine, but when I try to make the plot it just runs forever and when I stopped it (forced it to stop) I got the error message: no loop for break/next, jumping to top level
Any idea of what is going on?

Greate pacakge!!
Maria

ara = alpha_rare_all(
ps = physeq,
method = "Richness",
group = "intervention")