diff --git a/Biobase/Taxonomy.hs b/Biobase/Taxonomy.hs --- a/Biobase/Taxonomy.hs +++ b/Biobase/Taxonomy.hs @@ -4,10 +4,8 @@ -- Datatypes used to represent taxonomy data module Biobase.Taxonomy.Types, module Biobase.Taxonomy.Import, - module Biobase.Taxonomy.Utils, - module Biobase.Taxonomy.Visualization + module Biobase.Taxonomy.Utils ) 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 deleted file mode 100644 --- a/Biobase/Taxonomy/Visualization.hs +++ /dev/null @@ -1,100 +0,0 @@ --- | 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 @@ -1,5 +1,9 @@ -*-change-log-*- +2.1.0 [Florian Eggenhofer](mailto:egg@cs.uni-freiburg.de) 17. December 2019 + + * Moved visualisation code to own library + 2.0.0 [Florian Eggenhofer](mailto:egg@cs.uni-freiburg.de) 18. November 2019 * Changed to Biobase repository layout diff --git a/Taxonomy.cabal b/Taxonomy.cabal --- a/Taxonomy.cabal +++ b/Taxonomy.cabal @@ -1,5 +1,5 @@ name: Taxonomy -version: 2.0.0 +version: 2.1.0 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 +Tested-With: GHC == 8.4.4, GHC == 8.6.5, GHC == 8.8.1 Extra-Source-Files: README.md ChangeLog.md @@ -38,16 +38,15 @@ source-repository this type: git - location: https://github.com/eggzilla/Taxonomy/tree/v2.0.0 - tag: v2.0.0 + location: https://github.com/eggzilla/Taxonomy/tree/v2.1.0 + tag: v2.1.0 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, graphviz>=2999.12.0.4, bytestring, aeson, vector + build-depends: base >=4.5 && <5, parsec, either-unwrap, fgl>=5.5.4.0, text, bytestring, aeson, vector Hs-source-dirs: . Exposed-modules: Biobase.Taxonomy.Types Biobase.Taxonomy.Import - Biobase.Taxonomy.Visualization Biobase.Taxonomy.Utils Biobase.Taxonomy