yongxinliu / microbiomestatplot Goto Github PK

Hi,
I got an error when trying to run the codes prepared in 252NetworkModule.Rmd:

plot(t_net_its,vertex.label=NA,vertex.size=tits_nodesizes, layout=coords_t_its, mark.groups=list(t_mods_list_cs$1,t_mods_list_cs$2,t_mods_list_cs$3,t_mods_list_cs$4,t_mods_list_cs$8), mark.col=t_cols, mark.border=t_cols)

Error in xspline(cl$rescoords, shape = shape, open = FALSE, col = col, :
unable to allocate memory (in xspline)

##############

I found there was no data in module 3 and 8. After I changed the original codes by removingt_mods_list_cs$3 and t_mods_list_cs$8 in mark.groups = list(), the problem was solved. However, I do not know why I got different results.
p1_network.pdf

Hi Yongxin,
Thank you for developing the package "amplicon". When I tried to install it, I got the following error and warnings. Do you have any suggestions on how to solve them? Thanks.

Error: Failed to install 'amplicon' from GitHub:
(converted from warning) unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.6:
cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.6/PACKAGES'
In addition: Warning messages:
1: In untar2(tarfile, files, list, exdir) :
skipping pax global extended headers
2: In untar2(tarfile, files, list, exdir) :
skipping pax global extended headers

在运行BetaDiv.R过程中
result = BetaDiv(otu, map, tree = tree,
dist = "bray", group = map$Group, method = "PCoA" ,
pvalue.cutoff = 0.05, Micromet = "adonis")
提示Error in h(simpleError(msg, call)) :
在为'sample_data'函数选择方法时评估'object'参数出了错: 选择了未定义的列
使用的是您的data种的otu_tab.txt和metadata
谢谢