lmc297 / bactaxr Goto Github PK

Hi,

I met some issue when I tried to install your package. I tried to use source, but I met another issues.
Thanks for your help!

R version 3.6.0 (2019-04-26)
install_github("lmc297/bactaxR")
Downloading GitHub repo lmc297/bactaxR@master
Skipping 1 packages not available: ggtree
checking DESCRIPTION meta-information ...6/m7k540fd0hq9bbhdzxshn2h40000gn/T/Rtmp8b2FOu/remotes140dd92d41db/lmc297-bactaxR-57fa45b/DESCRIPTION’ ...

• installing source package ‘bactaxR’ ...
  ** using staged installation
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** inst
  ** byte-compile and prepare package for lazy loading
  Erreur : (converti depuis l'avis) le package ‘ggtree’ a été compilé avec la version R 3.6.1
  Exécution arrêtée
  ERROR: lazy loading failed for package ‘bactaxR’
• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/bactaxR’
  Erreur : Failed to install 'bactaxR' from GitHub:
  (converti depuis l'avis) installation of package ‘/var/folders/06/m7k540fd0hq9bbhdzxshn2h40000gn/T//Rtmp8b2FOu/file140dd7a3e9591/bactaxR_0.1.0.tar.gz’ had non-zero exit status

Does it represent the ANI of that pair?
Or does edge weight represent the ANI?

Thank you!

I have successfully ran the package to generate a histogram, however when I am trying to generate the dendrogram I ran into the following error:

summary(ani)
An object of class bactaxRObject
Number of genomes: 60
Total number of pairwise ANI comparisons: 2231
h
dend <- ANI.dendrogram(bactaxRObject = ani, ANI_threshold = 94.2, xline = c(4,5,6,7.5), xlinecol = c("#ffc425", "#f37735", "deeppink4", "black"), label_size = 0.5)
Error in hclust(d = d.dist, method = "average") :
NA/NaN/Inf in foreign function call (arg 10)

I have checked my ani input does not contain any NA/NaN/Inf.

Please kindly help, thanks in advance.

Hello,

Thank you so much for developing and sharing this tool! I am trying to make a tree from fastANI pairwise data. After successfully importing the txt file, I received the following error when I ran dend <- ANI.dendrogram(bactaxRObject = ani, ANI_threshold = 95) on my dataset:

Error in hclust(d = d.dist, method = "average") :
NaN dissimilarity value.

I double-checked that my data dose not contain any NAs by running

is.na(ani@ANI)%>%sum()
[1] 0

I am just wondering if you have any insight on how to fix this and it seems like that the hclust command introduces some NAs. Thank you.

Best,
Jessi

I have the same problem of this R script.

summary(ani)
An object of class bactaxRObject
Number of genomes: 33
Total number of pairwise ANI comparisons: 1086> h <- ANI.histogram(bactaxRObject = ani, bindwidth = 0.1)
h
dend <- ANI.dendrogram(bactaxRObject = ani, ANI_threshold = 95, xline = c(4,5,6,7.5), xlinecol = c("#ffc425", "#f37735", "deeppink4", "black"), label_size = 0.5)

I did this one exactly but I get the error message.(Error in hclust(d = d.dist, method = "average") : NA/NaN/Inf in foreign function call (arg 10))
Also, I check the file and I can't find the NA/NaN/Inf
I don't understand what the NA/NaN/Inf mean,

Can you solve this problem, please.

dear @lmc297

First off, great package!!! I have been able to use this package and I am very happy with the results obtained.

Nevertheless, I was wondering if there is a way to extract the resulting dendrogram from the ANI.dendrogram function. I would be interested in furhter editing this dendrogram.

Cheers,
Pablo