src/Gargantext/Core/Viz/Phylo/View/Metrics.hs

   1 {-|
   2 Module      : Gargantext.Core.Viz.Phylo.Tools
   3 Description : Phylomemy Tools to build/manage it
   4 Copyright   : (c) CNRS, 2017-Present
   5 License     : AGPL + CECILL v3
   6 Maintainer  : team@gargantext.org
   7 Stability   : experimental
   8 Portability : POSIX
   9
  10
  11 -}
  12
  13
  14 module Gargantext.Core.Viz.Phylo.View.Metrics
  15   where
  16
  17 import Control.Lens     hiding (makeLenses, both, Level)
  18 import Data.List        (last,groupBy,sortOn)
  19 import Data.Map         (insert)
  20 import Data.Text        (Text)
  21 import Gargantext.Prelude
  22 import Gargantext.Core.Viz.Phylo
  23 import Gargantext.Core.Viz.Phylo.Tools
  24
  25
  26 -- | To add a new meta Metric to a PhyloBranch
  27 addBranchMetrics :: PhyloBranchId -> Text -> Double -> PhyloView -> PhyloView
  28 addBranchMetrics id lbl val v = over (pv_branches
  29                                      . traverse)
  30                                     (\b -> if getBranchId b == id
  31                                            then b & pb_metrics %~ insert lbl [val]
  32                                            else b) v
  33
  34
  35 branchGroups :: PhyloView -> PhyloView
  36 branchGroups v = foldl (\v' (bId,nb) -> addBranchMetrics bId "nbGroups" nb v') v
  37                $ map (\(bId,ns) -> (bId,fromIntegral $ length ns))
  38                $ getNodesByBranches v
  39
  40
  41 -- | To get the age (in year) of all the branches of a PhyloView
  42 branchAge :: PhyloView -> PhyloView
  43 branchAge v = foldl (\v' b -> let bId = (fst . (head' "branchAge")) b
  44                                   prds = sortOn fst $ map snd b
  45                               in addBranchMetrics bId "age" ((abs . fromIntegral) $ ((snd . last) prds) - (fst $ head' "branchAge" prds)) v') v
  46             $ groupBy ((==) `on` fst)
  47             $ sortOn fst
  48             $ map (\n -> (getNodeBranchId n, (fst . fst) $ getNodeId n))
  49             $ getNodesInBranches v
  50
  51
  52 -- | To get the age (in year) of all the branches of a PhyloView
  53 branchBirth :: PhyloView -> PhyloView
  54 branchBirth v = foldl (\v' b -> let bId = (fst . (head' "branchBirth")) b
  55                                     prds = sortOn fst $ map snd b
  56                               in addBranchMetrics bId "birth" (fromIntegral $ fst $ head' "branchAge" prds) v') v
  57             $ groupBy ((==) `on` fst)
  58             $ sortOn fst
  59             $ map (\n -> (getNodeBranchId n, (fst . fst) $ getNodeId n))
  60             $ getNodesInBranches v
  61
  62
  63 -- | To process a list of Metrics to a PhyloView
  64 processMetrics :: [Metric] -> Phylo -> PhyloView -> PhyloView
  65 processMetrics ms _p v = foldl (\v' m -> case m of
  66                                         BranchAge -> branchAge v'
  67                                         BranchBirth -> branchBirth v'
  68                                         BranchGroups -> branchGroups v'
  69                                        -- _         -> panic "[ERR][Viz.Phylo.Example.processMetrics] metric not found"
  70                                         ) v ms
  71
  72