too-many-cells 0.1.12.1 → 0.1.12.2

raw patch · 3 files changed

+26/−4 lines, 3 filesdep ~hierarchical-spectral-clustering

Dependency ranges changed: hierarchical-spectral-clustering

Files

• app/Main.hs +3/−1
• src/TooManyCells/Matrix/Utility.hs +20/−0
• too-many-cells.cabal +3/−3

@@ -101,7 +101,7 @@                , minModularity :: Maybe Double <?> "([Nothing] | DOUBLE) Nearly the same as --min-distance, but for clustering instead of drawing (so the output json tree can be larger). Stopping criteria to stop at the node with DOUBLE modularity. So a node N with L and R children will stop with this criteria the distance at N to L and R is < DOUBLE. Does not include 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."                , 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."+               , 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."                , 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."@@ -347,6 +347,8 @@      -- Check for empty matrix.     when (V.null . getRowNames $ processedSc) $ error "Matrix is empty. Check --filter-thresholds, --normalization, or the input matrix for over filtering or incorrect input format."++    liftIO . mapM_ print . matrixValidity $ processedSc      return processedSc 

@@ -22,6 +22,7 @@     , writeMatrixLike     , isCsvFile     , getMatrixOutputType+    , matrixValidity     ) where  -- Remote@@ -234,3 +235,22 @@ -- | Get matrix output format from input name. getMatrixOutputType :: FilePath -> MatrixFileFolder getMatrixOutputType x = bool (MatrixFolder x) (MatrixFile x) . isCsvFile $ x++-- | Check validity of matrix.+matrixValidity :: (MatrixLike a) => a -> Maybe String+matrixValidity mat+  | rows /= numCells || cols /= numFeatures =+      Just $ "Warning: mismatch in number of (features, cells) ("+                           <> show numFeatures+                           <> ","+                           <> show numCells+                           <> ") with matrix (rows, columns) ("+                           <> show cols+                           <> ","+                           <> show rows+                           <> "), will probably result in error."+  | otherwise = Nothing+  where+    (rows, cols) = S.dimSM . getMatrix $ mat+    numCells = V.length . getRowNames $ mat+    numFeatures = V.length . getColNames $ mat

@@ -1,6 +1,6 @@ cabal-version: >=1.10 name: too-many-cells-version: 0.1.12.1+version: 0.1.12.2 license: GPL-3 license-file: LICENSE copyright: 2019 Gregory W. Schwartz@@ -65,7 +65,7 @@         foldl >=1.4.2,         graphviz >=2999.20.0.2,         hierarchical-clustering >=0.4.6,-        hierarchical-spectral-clustering >=0.4.0.2,+        hierarchical-spectral-clustering >=0.4.1.1,         hmatrix >=0.19.0.0,         inline-r >=0.9.2,         lens >=4.16.1,@@ -114,7 +114,7 @@         filepath >=1.4.2,         find-clumpiness >=0.2.3.1,         graphviz >=2999.20.0.2,-        hierarchical-spectral-clustering >=0.4.0.2,+        hierarchical-spectral-clustering >=0.4.1.1,         inline-r >=0.9.2,         lens >=4.16.1,         matrix-market-attoparsec >=0.1.0.8,