too-many-cells 0.2.0.0 → 0.2.1.0
raw patch · 2 files changed
+7/−3 lines, 2 filesdep ~birch-beer
Dependency ranges changed: birch-beer
Files
- app/Main.hs +4/−0
- too-many-cells.cabal +3/−3
app/Main.hs view
@@ -120,6 +120,7 @@ , drawColors :: Maybe String <?> "([Nothing] | COLORS) Custom colors for the labels or continuous features. Will repeat if more labels than provided colors. For continuous feature plots, uses first two colors [high, low], defaults to [red, gray]. For instance: --draw-colors \"[\\\"#e41a1c\\\", \\\"#377eb8\\\"]\"" , drawDiscretize :: Maybe String <?> "([Nothing] | COLORS | INT) Discretize colors by finding the nearest color for each item and node. For instance, --draw-discretize \"[\\\"#e41a1c\\\", \\\"#377eb8\\\"]\" will change all node and item colors to one of those two colors, based on Euclidean distance. If using \"--draw-discretize INT\", will instead take the default map and segment (or interpolate) it into INT colors, rather than a more continuous color scheme. May have unintended results when used with --draw-scale-saturation." , drawScaleSaturation :: Maybe Double <?> "([Nothing] | DOUBLE) Multiply the saturation value all nodes by this number in the HSV model. Useful for seeing more visibly the continuous colors by making the colors deeper against a gray scale."+ , drawFont :: Maybe String <?> "([Arial] | FONT) Specify the font to use for the labels when plotting." , pca :: Maybe Int <?> "([Nothing] | INT) Not recommended, as it makes cosine similarity less meaningful (therefore less accurate -- instead, consider making your own similarity matrix and using cluster-tree, our sister algorithm, to cluster the matrix and plot with birch-beer). The number of dimensions to keep for PCA dimensionality reduction before clustering. Default is no PCA at all in order to keep all information. Should use with --shift-positive to ensure no negative values." , noFilter :: Bool <?> "Whether to bypass filtering genes and cells by low counts." , shiftPositive :: Bool <?> "Shift features to positive values. Positive values are shifted to allow modularity to work correctly."@@ -186,6 +187,7 @@ short "drawColors" = Just 'R' short "drawDendrogram" = Just 'D' short "drawDiscretize" = Nothing+ short "drawFont" = Nothing short "drawLeaf" = Just 'L' short "drawLegendAllLabels" = Just 'J' short "drawLegendSep" = Just 'Q'@@ -458,6 +460,7 @@ finalError err x = "Error in draw-discretize: " <> err <> " " <> x drawScaleSaturation' = fmap DrawScaleSaturation . unHelpful . drawScaleSaturation $ opts+ drawFont' = fmap DrawFont . unHelpful . drawFont $ opts order' = Order . fromMaybe 1 . unHelpful . order $ opts clumpinessMethod' = maybe Clump.Majority (readOrErr "Cannot read clumpiness-method.")@@ -584,6 +587,7 @@ , _birchDrawColors = drawColors' , _birchDrawDiscretize = drawDiscretize' , _birchDrawScaleSaturation = drawScaleSaturation'+ , _birchDrawFont = drawFont' , _birchTree = _clusterDend originalClusterResults , _birchMat = birchMat , _birchSimMat = birchSimMat
too-many-cells.cabal view
@@ -1,6 +1,6 @@ cabal-version: >=1.10 name: too-many-cells-version: 0.2.0.0+version: 0.2.1.0 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 >=0.2.0.0,+ birch-beer >=0.2.1.0, 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 >=0.2.0.0,+ birch-beer >=0.2.1.0, bytestring >=0.10.8.2, cassava >=0.5.1.0, colour >=2.3.4,