too-many-cells 0.1.4.0 → 0.1.5.0
raw patch · 2 files changed
+10/−6 lines, 2 filesdep ~birch-beer
Dependency ranges changed: birch-beer
Files
- app/Main.hs +7/−3
- too-many-cells.cabal +3/−3
app/Main.hs view
@@ -98,10 +98,11 @@ , 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."+ , 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."- , drawLeaf :: Maybe String <?> "([DrawText] | DrawItem DrawItemType) How to draw leaves in the dendrogram. DrawText is the number of items in that leaf. DrawItem is the collection of items represented by circles, consisting of: DrawItem DrawLabel, where each item is colored by its label, DrawItem (DrawContinuous FEATURE), where each item is colored by the expression of FEATURE (corresponding to a feature name in the input matrix), DrawItem (DrawThresholdContinuous [(FEATURE, DOUBLE)]), where each item is colored by the binary high / low expression of FEATURE based on DOUBLE and multiple FEATUREs can be used to combinatorically label items (FEATURE1 high / FEATURE2 low, etc.), DrawItem DrawSumContinuous, where each item is colored by the sum of the post-normalized columns (use --normalization NoneNorm for UMI counts, default), and DrawItem DrawDiversity, where each node is colored by the diversity based on the labels of each item and the color is normalized separately for the leaves and the inner nodes. The default is DrawText, unless --labels-file is provided, in which DrawItem DrawLabel is the default. If the label or feature cannot be found, the default color will be black (check your spelling!)."- , drawCollection :: Maybe String <?> "([PieChart] | PieRing | PieNone | CollectionGraph MAXWEIGHT THRESHOLD [NODE]) How to draw item leaves in the dendrogram. PieRing draws a pie chart ring around the items. PieChart only draws a pie chart instead of items. PieNone only draws items, no pie rings or charts. (CollectionGraph MAXWEIGHT THRESHOLD [NODE]) draws the nodes and edges within leaves that are descendents of NODE (empty list [] indicates draw all leaf networks) based on the input matrix, normalizes edges based on the MAXWEIGHT, and removes edges for display less than THRESHOLD (after normalization, so for CollectionGraph 2 0.5 [26], draw the leaf graphs for all leaves under node 26, then a edge of 0.7 would be removed because (0.7 / 2) < 0.5)."+ , drawLeaf :: Maybe String <?> "([DrawText] | DrawItem DrawItemType) How to draw leaves in the dendrogram. DrawText is the number of items in that leaf. DrawItem is the collection of items represented by circles, consisting of: DrawItem DrawLabel, where each item is colored by its label, DrawItem (DrawContinuous FEATURE), where each item is colored by the expression of FEATURE (corresponding to a feature name in the input matrix), DrawItem (DrawThresholdContinuous [(FEATURE, DOUBLE)]), where each item is colored by the binary high / low expression of FEATURE with cutoff DOUBLE (so a value 0 means low <= 0, high > 0) and multiple FEATUREs can be used to combinatorically label items (FEATURE1 high / FEATURE2 low, etc.), DrawItem DrawSumContinuous, where each item is colored by the sum of the post-normalized columns (use --normalization NoneNorm for UMI counts, default), and DrawItem DrawDiversity, where each node is colored by the diversity based on the labels of each item and the color is normalized separately for the leaves and the inner nodes. The default is DrawText, unless --labels-file is provided, in which DrawItem DrawLabel is the default. If the label or feature cannot be found, the default color will be black (check your spelling!)."+ , drawCollection :: Maybe String <?> "([PieChart] | PieRing | PieNone | CollectionGraph MAXWEIGHT THRESHOLD [NODE]) How to draw item leaves in the dendrogram. PieRing draws a pie chart ring around the items. PieChart only draws a pie chart instead of items. PieNone only draws items, no pie rings or charts. (CollectionGraph MAXWEIGHT THRESHOLD [NODE]) draws the nodes and edges within leaves that are descendents of NODE (empty list [] indicates draw all leaf networks) based on the input matrix, normalizes edges based on the MAXWEIGHT, and removes edges for display less than THRESHOLD (after normalization, so for CollectionGraph 2 0.5 [26], draw the leaf graphs for all leaves under node 26, then a edge of 0.7 would be removed because (0.7 / 2) < 0.5). For CollectionGraph with no colors, use --draw-leaf \"DrawItem DrawLabel\" and all nodes will be black. If you don't specify this option, DrawText from --draw-leaf overrides this argument and only the number of cells will be plotted." , drawMark :: Maybe String <?> "([MarkNone] | MarkModularity) How to draw annotations around each inner node in the tree. MarkNone draws nothing and MarkModularity draws a black circle representing the modularity at that node, darker black means higher modularity for that next split." , drawNodeNumber :: Bool <?> "Draw the node numbers on top of each node in the graph." , drawMaxNodeSize :: Maybe Double <?> "([72] | DOUBLE) The max node size when drawing the graph. 36 is the theoretical default, but here 72 makes for thicker branches."@@ -140,7 +141,7 @@ , delimiter :: Maybe Char <?> "([,] | CHAR) The delimiter for the csv file if using a normal csv rather than cellranger output and for --labels-file." , normalization :: Maybe String <?> "([TfIdfNorm] | UQNorm | MedNorm | TotalMedNorm | BothNorm | NoneNorm) Type of normalization before clustering. TfIdfNorm normalizes based on the prevalence of each feature. UQNorm normalizes each observation by the upper quartile non-zero counts of that observation. MedNorm normalizes each observation by the median non-zero counts of that observation. TotalMedNorm normalized first each observation by total count then by median of non-zero counts across features. BothNorm uses both normalizations (first TotalMedNorm for all analysis then additionally TfIdfNorm during clustering). NoneNorm does not normalize. Default is TfIdfNorm for clustering and NoneNorm for differential (which instead uses the recommended edgeR single cell preprocessing including normalization and filtering, any normalization provided here will result in edgeR preprocessing on top). Cannot use TfIdfNorm for any other process as NoneNorm will become the default." , prior :: Maybe String <?> "([Nothing] | STRING) The input folder containing the output from a previous run. If specified, skips clustering by using the previous clustering files."- , nodes :: String <?> "([NODE], [NODE]) Find the differential expression between cells belonging downstream of a list of nodes versus another list of nodes. \"([], [])\" switches the process to instead find the log2 average division between all nodes with all other cells (node / other cells) using the Kruskal-Wallis Test (--genes does not work for this, --labels works, and UQNorm for the normalization is recommended. Only returns nodes where the comparison had both groups containing at least five cells.)."+ , nodes :: String <?> "([NODE], [NODE]) Find the differential expression between cells belonging downstream of a list of nodes versus another list of nodes. Directionality is \"([1], [2])\" -> 2 / 1. \"([], [])\" switches the process to instead find the log2 average division between all nodes with all other cells (node / other cells) using the Kruskal-Wallis Test (--genes does not work for this, --labels works, and UQNorm for the normalization is recommended. Only returns nodes where the comparison had both groups containing at least five cells.)." , labels :: Maybe String <?> "([Nothing] | ([LABEL], [LABEL])) Use --labels-file to restrict the differential analysis to cells with these labels. Same format as --nodes, so the first list in --nodes and --labels gets the cells within that list of nodes with this list of labels. The same for the second list. For instance, --nodes \"([1], [2])\" --labels \"([\\\"A\\\"], [\\\"B\\\"])\" will compare cells from node 1 of label \"A\" only with cells from node 2 of label \"B\" only. To use all cells for that set of nodes, use an empty list, i.e. --labels \"([], [\\\"A\\\"])\". When comparing all nodes with all other cells, remember that the notation would be ([Other Cells], [Node]), so to compare cells of label X in Node with cells of label Y in Other Cells, use --labels \"([\\\"Y\\\", \\\"X\\\"])\". Requires both --labels and --labels-file, otherwise will include all labels." , topN :: Maybe Int <?> "([100] | INT ) The top INT differentially expressed genes." , genes :: [T.Text] <?> "([Nothing] | GENE) List of genes to plot for all cells within selected nodes. Invoked by --genes CD4 --genes CD8 etc. When this argument is supplied, only the plot is outputted and edgeR differential expression is ignored. Outputs to --output."@@ -165,6 +166,7 @@ modifiers :: Modifiers modifiers = lispCaseModifiers { shortNameModifier = short } where+ short "customCut" = Nothing short "clumpinessMethod" = Just 'u' short "clusterNormalization" = Just 'C' short "dendrogramOutput" = Just 'U'@@ -346,6 +348,7 @@ fmap MaxProportion . unHelpful . maxProportion $ opts minDistance' = fmap MinDistance . unHelpful . minDistance $ opts smartCutoff' = fmap SmartCutoff . unHelpful . smartCutoff $ opts+ customCut' = CustomCut . Set.fromList . unHelpful . customCut $ opts dendrogramOutput' = DendrogramFile . fromMaybe "dendrogram.svg" . unHelpful@@ -513,6 +516,7 @@ , _birchMaxProportion = maxProportion' , _birchMinDistance = minDistance' , _birchSmartCutoff = smartCutoff'+ , _birchCustomCut = customCut' , _birchOrder = Just order' , _birchDrawLeaf = drawLeaf' , _birchDrawCollection = drawCollection'
too-many-cells.cabal view
@@ -1,6 +1,6 @@ cabal-version: >=1.10 name: too-many-cells-version: 0.1.4.0+version: 0.1.5.0 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 >=0.1.0.1,+ birch-beer >=0.1.1.1, 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 >=0.1.0.1,+ birch-beer >=0.1.1.1, bytestring >=0.10.8.2, cassava >=0.5.1.0, colour >=2.3.4,