Debug biom file load, change biomformat library

LoadPackages.R

@@ -47,16 +47,17 @@ if (!require(d3heatmap)) {
   library(d3heatmap)
 }
 
-if (!require(biom)) {
-  install.packages('biom')
-  library(biom)
-}
-
 if (!require(devtools)) {
   install.packages('devtools')
   library(devtools)
 }
 
+# Let us use biomformat instead of biom
+if (!require(biomformat)){
+ library(biomformat)
+ devtools::install_github("biomformat", "aghozlane")
+}
+
 if (!require(scatterD3)) {
   install.packages('scatterD3')
   library(scatterD3)

internal.R

@@ -125,15 +125,14 @@ CheckCountsTable <- function(counts)
     ## Taxonomy table
     taxo = as.data.frame(observation_metadata(dataBIOM))
     OTUnames = rownames(taxo)
-
     ## Modif taxo table (remove p__,... and change the colnames)
     taxo = as.data.frame(sapply(taxo,gsub,pattern="^.*__",replacement=""))
     colnames(taxo) = c("Kingdom", "Phylum","Class","Order","Family","Genus","Species")
     rownames(taxo) = OTUnames
     ## Remove empty row
     taxo[taxo==""] = NA
-    taxo = na.omit(taxo)
-    
+    taxo[taxo=="Unassigned"] = NA
+    taxo=taxo[rowSums(is.na(taxo))!=dim(taxo)[2], ]
     
     CheckTaxo = CheckTaxoTable(taxo,counts)