too-many-cells 0.1.7.1 → 0.1.8.0
raw patch · 2 files changed
+9/−5 lines, 2 filesdep ~birch-beer
Dependency ranges changed: birch-beer
Files
- app/Main.hs +6/−2
- too-many-cells.cabal +3/−3
app/Main.hs view
@@ -97,7 +97,8 @@ , maxStep :: Maybe Int <?> "([Nothing] | INT) Only keep clusters that are INT steps from the root. Defaults to all steps." , maxProportion :: Maybe Double <?> "([Nothing] | DOUBLE) Stopping criteria to stop at the node immediate after a node with DOUBLE proportion split. So a node N with L and R children will stop with this criteria at 0.5 if |L| / |R| < 0.5 or > 2 (absolute log2 transformed), that is, if one child has over twice as many items as the other child. Includes L and R in the final result." , minDistance :: Maybe Double <?> "([Nothing] | DOUBLE) Stopping criteria to stop at the node immediate after a node with DOUBLE distance. So a node N with L and R children will stop with this criteria the distance at N to L and R is < DOUBLE. Includes L and R in the final result."- , smartCutoff :: Maybe Double <?> "([Nothing] | DOUBLE) Whether to set the cutoffs for --min-size, --max-proportion, and --min-distance based off of the distributions (median + (DOUBLE * MAD)) of all nodes. To use smart cutoffs, use this argument and then set one of the three arguments to an arbitrary number, whichever cutoff type you want to use. --min-size distribution is log2 transformed."+ , 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 three arguments to an arbitrary number, whichever cutoff type you want to use. --min-size 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." , 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 in matrix market format or, if a csv file is specified, a dense csv format."@@ -196,6 +197,7 @@ short "maxProportion" = Just 'X' short "maxStep" = Just 'S' short "minDistance" = Nothing+ short "minDistanceSearch" = Nothing short "minSize" = Just 'M' short "noFilter" = Just 'F' short "normalization" = Just 'z'@@ -350,7 +352,8 @@ maxStep' = fmap MaxStep . unHelpful . maxStep $ opts maxProportion' = fmap MaxProportion . unHelpful . maxProportion $ opts- minDistance' = fmap MinDistance . unHelpful . minDistance $ opts+ minDistance' = fmap MinDistance . unHelpful . minDistance $ opts+ minDistanceSearch' = fmap MinDistanceSearch . unHelpful . minDistanceSearch $ opts smartCutoff' = fmap SmartCutoff . unHelpful . smartCutoff $ opts customCut' = CustomCut . Set.fromList . unHelpful . customCut $ opts dendrogramOutput' = DendrogramFile@@ -534,6 +537,7 @@ , _birchMaxStep = maxStep' , _birchMaxProportion = maxProportion' , _birchMinDistance = minDistance'+ , _birchMinDistanceSearch = minDistanceSearch' , _birchSmartCutoff = smartCutoff' , _birchCustomCut = customCut' , _birchOrder = Just order'
too-many-cells.cabal view
@@ -1,6 +1,6 @@ cabal-version: >=1.10 name: too-many-cells-version: 0.1.7.1+version: 0.1.8.0 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 >=0.1.3.1,+ birch-beer >=0.1.4.0, bytestring >=0.10.8.2, cassava >=0.5.1.0, colour >=2.3.4,@@ -103,7 +103,7 @@ base >=4.11.1.0, too-many-cells -any, aeson >=1.4.0.0,- birch-beer >=0.1.3.1,+ birch-beer >=0.1.4.0, bytestring >=0.10.8.2, cassava >=0.5.1.0, colour >=2.3.4,