Genetic Diversity Module - Server Function

Assembles the live breeding-group, genetic-value, and kinship reactive inputs into the per-group heat-map statistics (via getGeneticDiversityStats) and renders the red/yellow/green heat map (via makeGeneticDiversityHeatmap). When breeding groups have not been formed or the genetic value analysis has not been run, the module shows guidance instead of an empty plot. When a formed group holds an animal the loaded pedigree no longer has (a new file was read, or the view was trimmed, after the groups were formed), the page says so in one sentence and asks for the groups to be formed again; any other calculation error is shown once, where the heat map would be. When any animal in the groups has no birth date, a note under the heat map says how many, and how many females among them the Production and Inbreeding columns counted (those the pedigree lists as a dam) and left out.

Usage

modGeneticDiversityServer(
  id,
  groups,
  pedigree,
  geneticValues,
  kinshipMatrix,
  currentDate = Sys.Date()
)

Arguments

id

character vector of length 1. Module namespace identifier.

groups

reactive returning a list of character vectors of animal IDs, one per breeding group (the groups returned by modBreedingGroupsServer). That list includes the trailing "Unused" element when candidates remain unplaced, and the heat map scores it as another group. If the list is named, the names are the heat map's row labels (the app passes the names that the Breeding Groups module returns as groupLabels, so the last row reads "Unused animals"); an unnamed list gives "Group 1", "Group 2" and so on.

pedigree

reactive returning the quality-controlled pedigree data frame.

geneticValues

reactive returning the genetic value report data frame (with id and value columns).

kinshipMatrix

reactive returning a square kinship matrix (row and column names are animal IDs) covering every member of every group; getGeneticDiversityStats stops when a group member is missing from it. In the app this is the full-pedigree kinship matrix that Summary Statistics and Breeding Groups also use, so it covers every animal of the pedigree, not only the Genetic Value population.

currentDate

Date used to derive age and the production birth window. Defaults to Sys.Date().

Value

A list with two reactive elements: stats, the per-group metric data frame (or NULL when data are not ready), and heatmap, the ggplot heat map (or NULL). Errors raised inside getGeneticDiversityStats (a group member missing from the kinship matrix) are not caught, so the reactives error instead of returning NULL.

See also

modGeneticDiversityUI

Other Shiny modules: modBreedingGroupsServer(), modBreedingGroupsUI(), modCrossCenterIdentityServer(), modCrossCenterIdentityUI(), modDeidentifiedExportServer(), modDeidentifiedExportUI(), modGeneticDiversityUI(), modGeneticValueServer(), modGeneticValueUI(), modGvAndBgDescServer(), modGvAndBgDescUI(), modInputServer(), modInputUI(), modMarkerGeneticsServer(), modMarkerGeneticsUI(), modMatePairServer(), modMatePairUI(), modORIPReportingServer(), modORIPReportingUI(), modPedigreeServer(), modPedigreeUI(), modPotentialParentsServer(), modPotentialParentsUI(), modPyramidServer(), modPyramidUI(), modSnapshotTrendsServer(), modSnapshotTrendsUI(), modSummaryStatsServer(), modSummaryStatsUI()