Curation coverage functions

[wdahdul]

These pertain to the data science/statistics user story "Curation Coverage"

1. function for reporting a summary of the data annotated in the KB for a taxon or list of taxa. In addition to taxon name and number of phenotypes, also include the family and order of each taxon.

2. function for reporting the entities annotated for a taxon or list of taxa. Include entity name and number of phenotypes.This is similar to the “print_coverage” function in paramo (copied below), although that function extracts information from a matrix including inferred data.

#' Function to display the number of matching species and average value across them from an Ontotrace matrix
#' @export
print_coverage <- function(x){
  coverage <- apply(x, 2, function(x) sum(!is.na(x)))
  average <- sapply(x, function(x) mean(as.numeric(na.omit(x[x %in% c("0", "1")])), na.rm=TRUE))
  cover <- cbind(coverage, average)
  tmp <- filter(data.frame(traits=rownames(cover), cover), coverage > 0, average < 1, average > 0) %>% arrange(., desc(coverage))
  print(tmp)
}
#The table that prints out shows the number of taxa for which there is data in the KB ( coverage ) and the proportion of taxa ( average ) that have this trait (all of these are binary, presence/absence characters).

[hlapp]

@wdahdul could you comment on how important you would consider having this for the upcoming 2023 TraitFest event?