Scott Handley shandley
shandley
/ gist:87b0017ca593c58561a8b76b98985477
Created
May 10, 2018 16:19
Convert Phyloseq to AmpVis2 format in R
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| ```{r phyloseq-ampvis2} | |
| library("ampvis2") | |
| # Load data into ampvis | |
| otu.table <- t(otu_table(ps1, taxa_are_rows = FALSE)) | |
| otu.table <- as.data.frame(otu.table) | |
| otu.table <- rownames_to_column(otu.table, var = "OTU") | |
| head(rownames(otu.table)) | |
| head(colnames(otu.table)) | |
| nrow(otu.table) |
shandley
/ centos_microbiome_setup.txt
Last active
July 25, 2017 21:41
Setting up R for microbiome analysis on a new Cent OS server
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| ## For CentOS | |
| sudo yum install libcurl-devel | |
| ## For R | |
| # Make R package path permissions usable | |
| # Identify the path using ... | |
| installed.packages()[, "LibPath"] | |
| ... and then update according to your server user permissions |