phenoscape / scate-shortcourse

Package for the "Phylogenetic comparative analysis of integrated anatomical traits" short course
http://phenoscape.org/scate-shortcourse/
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Error in line 338, amalgamation on individual traits #17

Closed wdahdul closed 5 years ago

wdahdul commented 5 years ago
> data(EF.maps)
> data(BR.maps)
> #########
> # Individual Traits Level
> ########
> # Set up a pretty color palette
> hm.palette <- colorRampPalette(brewer.pal(9, 'Set1'), space='Lab')
> 
> par(mfrow=c(1,2))
> ymax <- 1.1*length(td.comb$phy$tip.label) #set our boundaries for our plot area
> for(i in (1:length(char_info_comb$ID))){
+   trait <- char_info_comb$ID[i]
+   trait <- gsub(" ", "_", trait)
+   map <- paramo(trait, ntrees=1, dirW=dirW)
+   states <- unique(names(unlist(map[[1]]$maps)))
+   print(states)
+   try(plotSimmap(map[[1]], pts=F,ftype="off", colors=setNames(hm.palette(length(states)), states), ylim=c(0, ymax)))
+   title(paste0("\n ", trait))
+ }
Error in paramo(trait, ntrees = 1, dirW = dirW) : 
  could not find function "paramo"