diff --git a/Biobase/Taxonomy.hs b/Biobase/Taxonomy.hs --- a/Biobase/Taxonomy.hs +++ b/Biobase/Taxonomy.hs @@ -4,8 +4,10 @@ -- Datatypes used to represent taxonomy data module Biobase.Taxonomy.Types, module Biobase.Taxonomy.Import, - module Biobase.Taxonomy.Utils + module Biobase.Taxonomy.Utils, + module Biobase.Taxonomy.Visualization ) where import Biobase.Taxonomy.Types import Biobase.Taxonomy.Import import Biobase.Taxonomy.Utils +import Biobase.Taxonomy.Visualization diff --git a/Biobase/Taxonomy/Visualization.hs b/Biobase/Taxonomy/Visualization.hs new file mode 100644 --- /dev/null +++ b/Biobase/Taxonomy/Visualization.hs @@ -0,0 +1,101 @@ +-- | Functions for visualization of taxonomy data. +module Biobase.Taxonomy.Visualization ( -- * Datatypes + -- Datatypes used to represent taxonomy data + module Biobase.Taxonomy.Types, + -- * Visualization + drawTaxonomyComparison, + drawTaxonomy, + writeTree, + writeDotTree, + writeJsonTree + ) where +import Prelude +import Biobase.Taxonomy.Types +import Data.Graph.Inductive.Tree +import Data.Graph.Inductive.Basic +import qualified Data.GraphViz as GV +import qualified Data.GraphViz.Printing as GVP +import qualified Data.GraphViz.Attributes.Colors as GVAC +import qualified Data.GraphViz.Attributes.Complete as GVA +import qualified Data.ByteString.Lazy.Char8 as L +import qualified Data.Aeson as AE +import qualified Data.Text.Lazy as T + +--------------------------------------- +-- Visualisation functions + +-- | Draw graph in dot format. Used in Ids2Tree tool. +drawTaxonomy :: Bool -> Gr SimpleTaxon Double -> String +drawTaxonomy withRank inputGraph = do + let nodeFormating = if withRank then nodeFormatWithRank else nodeFormatWithoutRank + let params = GV.nonClusteredParams {GV.isDirected = True + , GV.globalAttributes = [GV.GraphAttrs [GVA.Size (GVA.GSize (20 :: Double) (Just (20 :: Double)) False)]] + , GV.isDotCluster = const True + --, GV.fmtNode = \ (_,l) -> [GV.textLabel (TL.pack (show (simpleRank l) ++ "\n" ++ T.unpack (simpleScientificName l)))] + , GV.fmtNode = nodeFormating + , GV.fmtEdge = const [] + } + let dotFormat = GV.graphToDot params inputGraph + let dottext = GVP.renderDot $ GVP.toDot dotFormat + T.unpack dottext + +nodeFormatWithRank :: (t, SimpleTaxon) -> [GVA.Attribute] +nodeFormatWithRank (_,l) = [GV.textLabel (T.concat [T.pack (show (simpleRank l)), T.pack ("\n") , simpleScientificName l])] + +nodeFormatWithoutRank :: (t, SimpleTaxon) -> [GVA.Attribute] +nodeFormatWithoutRank (_,l) = [GV.textLabel (simpleScientificName l)] + +-- | Draw tree comparison graph in dot format. Used in Ids2TreeCompare tool. +drawTaxonomyComparison :: Bool -> (Int,Gr CompareTaxon Double) -> String +drawTaxonomyComparison withRank (treeNumber,inputGraph) = do + let cList = makeColorList treeNumber + let nodeFormating = if withRank then (compareNodeFormatWithRank cList) else (compareNodeFormatWithoutRank cList) + let params = GV.nonClusteredParams {GV.isDirected = True + , GV.globalAttributes = [] + , GV.isDotCluster = const True + --, GV.fmtNode = \ (_,l) -> [GV.textLabel (TL.pack (show (compareRank l) ++ "\n" ++ B.unpack (compareScientificName l))), GV.style GV.wedged, GVA.Color (selectColors (inTree l) cList)] + , GV.fmtNode = nodeFormating + , GV.fmtEdge = const [] + } + let dotFormat = GV.graphToDot params (grev inputGraph) + let dottext = GVP.renderDot $ GVP.toDot dotFormat + T.unpack dottext + +compareNodeFormatWithRank :: [GVA.Color] -> (t, CompareTaxon) -> [GVA.Attribute] +compareNodeFormatWithRank cList (_,l) = [GV.textLabel (T.concat [T.pack (show (compareRank l) ++ "\n"),compareScientificName l]), GV.style GV.wedged, GVA.Color (selectColors (inTree l) cList)] + +compareNodeFormatWithoutRank :: [GVA.Color] -> (t, CompareTaxon) -> [GVA.Attribute] +compareNodeFormatWithoutRank cList (_,l) = [GV.textLabel (compareScientificName l), GV.style GV.wedged, GVA.Color (selectColors (inTree l) cList)] + +-- | Colors from color list are selected according to in which of the compared trees the node is contained. +selectColors :: [Int] -> [GVA.Color] -> GVAC.ColorList +selectColors inTrees currentColorList = GVAC.toColorList (map (\i -> currentColorList !! i) inTrees) + +-- | A color list is sampled from the spectrum according to how many trees are compared. +makeColorList :: Int -> [GVA.Color] +makeColorList treeNumber = cList + where cList = map (\i -> GVAC.HSV ((fromIntegral i/fromIntegral neededColors) * 0.708) 0.5 1.0) [0..neededColors] + neededColors = treeNumber - 1 + +-- | Write tree representation either as dot or json to provided file path +writeTree :: String -> String -> Bool -> Gr SimpleTaxon Double -> IO () +writeTree requestedFormat outputDirectoryPath withRank inputGraph = do + case requestedFormat of + "dot" -> writeDotTree outputDirectoryPath withRank inputGraph + "json"-> writeJsonTree outputDirectoryPath inputGraph + _ -> writeDotTree outputDirectoryPath withRank inputGraph + +-- | Write tree representation as dot to provided file path. +-- Graphviz tools like dot can be applied to the written .dot file to generate e.g. svg-format images. +writeDotTree :: String -> Bool -> Gr SimpleTaxon Double -> IO () +writeDotTree outputDirectoryPath withRank inputGraph = do + let diagram = drawTaxonomy withRank (grev inputGraph) + writeFile (outputDirectoryPath ++ "taxonomy.dot") diagram + +-- | Write tree representation as json to provided file path. +-- You can visualize the result for example with 3Djs. +writeJsonTree :: String -> Gr SimpleTaxon Double -> IO () +writeJsonTree outputDirectoryPath inputGraph = do + let jsonOutput = AE.encode (grev inputGraph) + L.writeFile (outputDirectoryPath ++ "taxonomy.json") jsonOutput + diff --git a/ChangeLog.md b/ChangeLog.md --- a/ChangeLog.md +++ b/ChangeLog.md @@ -1,4 +1,7 @@ -*-change-log-*- +2.2.0 [Florian Eggenhofer](mailto:egg@cs.uni-freiburg.de) 30. May 2020 + + * Compatibility with 9.0.1, reintegrated visualisation libraries 2.1.0 [Florian Eggenhofer](mailto:egg@cs.uni-freiburg.de) 17. December 2019 diff --git a/Taxonomy.cabal b/Taxonomy.cabal --- a/Taxonomy.cabal +++ b/Taxonomy.cabal @@ -1,5 +1,5 @@ name: Taxonomy -version: 2.1.0 +version: 2.2.0 synopsis: Libary for parsing, processing and vizualization of taxonomy data description: Haskell cabal Taxonomy libary contains tools, parsers, datastructures and visualisation for the NCBI (National Center for Biotechnology Information) Taxonomy datasources. @@ -27,7 +27,7 @@ category: Bioinformatics build-type: Simple cabal-version: >=1.10.0 -Tested-With: GHC == 8.4.4, GHC == 8.6.5, GHC == 8.8.1 +Tested-With: GHC == 8.4.4, GHC == 8.6.5, GHC == 8.8.1, GHC == 9.0.1 Extra-Source-Files: README.md ChangeLog.md @@ -38,15 +38,16 @@ source-repository this type: git - location: https://github.com/eggzilla/Taxonomy/tree/v2.1.0 - tag: v2.1.0 + location: https://github.com/eggzilla/Taxonomy/tree/v2.2.0 + tag: v2.2.0 Library ghc-options: -Wall -fno-warn-unused-do-bind default-language: Haskell2010 - build-depends: base >=4.5 && <5, parsec, either-unwrap, fgl>=5.5.4.0, text, bytestring, aeson, vector + build-depends: base >=4.5 && <5, parsec, either-unwrap, fgl>=5.5.4.0, text, bytestring, aeson, vector, graphviz Hs-source-dirs: . Exposed-modules: Biobase.Taxonomy.Types Biobase.Taxonomy.Import Biobase.Taxonomy.Utils + Biobase.Taxonomy.Visualization Biobase.Taxonomy