too-many-cells 0.2.1.0 → 0.2.2.0

raw patch · 2 files changed

+8/−4 lines, 2 filesdep ~birch-beer

Dependency ranges changed: birch-beer

Files

• app/Main.hs +5/−1
• too-many-cells.cabal +3/−3

@@ -104,6 +104,7 @@                , minDistanceSearch :: Maybe Double <?> "([Nothing] | DOUBLE) Similar to --min-distance, but searches from the leaves to the root -- if a path from a subtree contains a distance of at least DOUBLE, keep that path, otherwise prune it. This argument assists in finding distant nodes."                , smartCutoff :: Maybe Double <?> "([Nothing] | DOUBLE) Whether to set the cutoffs for --min-size, --max-proportion, --min-distance, and --min-distance-search based off of the distributions (median + (DOUBLE * MAD)) of all nodes. To use smart cutoffs, use this argument and then set one of the four arguments to an arbitrary number, whichever cutoff type you want to use. --min-proportion distribution is log2 transformed."                , customCut :: [Int] <?> "([Nothing] | NODE) List of nodes to prune (make these nodes leaves). Invoked by --custom-cut 34 --custom-cut 65 etc."+               , rootCut :: Maybe Int <?> "([Nothing] | NODE) Assign a new root to the tree, removing all nodes outside of the subtree."                , dendrogramOutput :: Maybe String <?> "([dendrogram.svg] | FILE) The filename for the dendrogram. Supported formats are PNG, PS, PDF, and SVG."                , matrixOutput :: Maybe String <?> "([Nothing] | FOLDER | FILE.csv) Output the filtered and normalized (not including TfIdfNorm) matrix in this folder under the --output directory in matrix market format or, if a csv file is specified, a dense csv format. Like input, features are rows. See --matrix-output-transpose."                , matrixOutputTranspose :: Maybe String <?> "([Nothing] | FOLDER | FILE.csv) Output the filtered and normalized (not including TfIdfNorm) matrix in this folder under the --output directory in matrix market format or, if a csv file is specified, a dense csv format. Differs from --matrix-output in that features are columns.columns."@@ -220,7 +221,8 @@     short "plotOutput"           = Nothing     short "priors"               = Just 'P'     short "projectionFile"       = Just 'j'-    short "shiftPositive"      = Nothing+    short "rootCut"              = Nothing+    short "shiftPositive"        = Nothing     short x                      = firstLetter x  instance ParseRecord Options where@@ -384,6 +386,7 @@         minDistanceSearch' = fmap MinDistanceSearch . unHelpful . minDistanceSearch $ opts         smartCutoff'      = fmap SmartCutoff . unHelpful . smartCutoff $ opts         customCut'        = CustomCut . Set.fromList . unHelpful . customCut $ opts+        rootCut'          = fmap RootCut . unHelpful . rootCut $ opts         dendrogramOutput' = DendrogramFile                           . fromMaybe "dendrogram.svg"                           . unHelpful@@ -573,6 +576,7 @@                     , _birchMinDistanceSearch   = minDistanceSearch'                     , _birchSmartCutoff = smartCutoff'                     , _birchCustomCut   = customCut'+                    , _birchRootCut     = rootCut'                     , _birchOrder = Just order'                     , _birchDrawLeaf = drawLeaf'                     , _birchDrawCollection = drawCollection'

@@ -1,6 +1,6 @@ cabal-version: >=1.10 name: too-many-cells-version: 0.2.1.0+version: 0.2.2.0 license: GPL-3 license-file: LICENSE copyright: 2019 Gregory W. Schwartz@@ -46,7 +46,7 @@     build-depends:         base >=4.7 && <5,         aeson >=1.4.0.0,-        birch-beer >=0.2.1.0,+        birch-beer >=0.2.2.0,         bytestring >=0.10.8.2,         cassava >=0.5.1.0,         colour >=2.3.4,@@ -102,7 +102,7 @@         base >=4.11.1.0,         too-many-cells -any,         aeson >=1.4.0.0,-        birch-beer >=0.2.1.0,+        birch-beer >=0.2.2.0,         bytestring >=0.10.8.2,         cassava >=0.5.1.0,         colour >=2.3.4,