rdkit.ML.Cluster.ClusterVis module — The RDKit 2016.09.1 documentation

# rdkit.ML.Cluster.ClusterVis module

Cluster tree visualization using Sping

class `rdkit.ML.Cluster.ClusterVis.` `ClusterRenderer`(canvas, size, ptColors=[], lineWidth=None, showIndices=0, showNodes=1, stopAtCentroids=0, logScale=0, tooClose=-1)

  Bases: `object`

  `DrawTree`(cluster, minHeight=2.0)

`rdkit.ML.Cluster.ClusterVis.` `ClusterToImg`(cluster, fileName, size=(300, 300), ptColors=[], lineWidth=None, showIndices=0, stopAtCentroids=0, logScale=0)

  handles the work of drawing a cluster tree to an image file

  > Arguments

  > > - cluster: the cluster tree to be drawn
  > > - fileName: the name of the file to be created
  > > - size: the size of output canvas
  > > - ptColors: if this is specified, the _colors_ will be used to color the terminal nodes of the cluster tree. (color == _pid.Color_)
  > > - lineWidth: if specified, it will be used for the widths of the lines used to draw the tree

  Notes

  > - The extension on _fileName_ determines the type of image file created. All formats supported by PIL can be used.
  > - if _ptColors_ is the wrong length for the number of possible terminal node types, this will throw an IndexError
  > - terminal node types are determined using their _GetData()_ methods

`rdkit.ML.Cluster.ClusterVis.` `ClusterToPDF`(cluster, fileName, size=(300, 300), ptColors=[], lineWidth=None, showIndices=0, stopAtCentroids=0, logScale=0)

  handles the work of drawing a cluster tree to an PDF file

  > Arguments

  > > - cluster: the cluster tree to be drawn
  > > - fileName: the name of the file to be created
  > > - size: the size of output canvas
  > > - ptColors: if this is specified, the _colors_ will be used to color the terminal nodes of the cluster tree. (color == _pid.Color_)
  > > - lineWidth: if specified, it will be used for the widths of the lines used to draw the tree

  Notes

  > - if _ptColors_ is the wrong length for the number of possible terminal node types, this will throw an IndexError
  > - terminal node types are determined using their _GetData()_ methods

`rdkit.ML.Cluster.ClusterVis.` `ClusterToSVG`(cluster, fileName, size=(300, 300), ptColors=[], lineWidth=None, showIndices=0, stopAtCentroids=0, logScale=0)

  handles the work of drawing a cluster tree to an SVG file

  > Arguments

  > > - cluster: the cluster tree to be drawn
  > > - fileName: the name of the file to be created
  > > - size: the size of output canvas
  > > - ptColors: if this is specified, the _colors_ will be used to color the terminal nodes of the cluster tree. (color == _pid.Color_)
  > > - lineWidth: if specified, it will be used for the widths of the lines used to draw the tree

  Notes

  > - if _ptColors_ is the wrong length for the number of possible terminal node types, this will throw an IndexError
  > - terminal node types are determined using their _GetData()_ methods

`rdkit.ML.Cluster.ClusterVis.` `DrawClusterTree`(cluster, canvas, size, ptColors=[], lineWidth=None, showIndices=0, showNodes=1, stopAtCentroids=0, logScale=0, tooClose=-1)

  handles the work of drawing a cluster tree on a Sping canvas

  > Arguments

  > > - cluster: the cluster tree to be drawn
  > > - canvas: the Sping canvas on which to draw
  > > - size: the size of _canvas_
  > > - ptColors: if this is specified, the _colors_ will be used to color the terminal nodes of the cluster tree. (color == _pid.Color_)
  > > - lineWidth: if specified, it will be used for the widths of the lines used to draw the tree

  Notes

  > - _Canvas_ is neither _save_d nor _flush_ed at the end of this
  > - if _ptColors_ is the wrong length for the number of possible terminal node types, this will throw an IndexError
  > - terminal node types are determined using their _GetData()_ methods

class `rdkit.ML.Cluster.ClusterVis.` `VisOpts`

  Bases: `object`

  stores visualization options for cluster viewing

  Instance variables

  > - x/yOffset: amount by which the drawing is offset from the edges of the canvas
  > - lineColor: default color for drawing the cluster tree
  > - lineWidth: the width of the lines used to draw the tree

  `hideColor` = Color(0.80,0.80,0.80)
  `hideWidth` = 1.1
  `highlightColor` = Color(1.00,1.00,0.40)
  `highlightRad` = 10
  `lineColor` = Color(0.00,0.00,0.00)
  `lineWidth` = 2
  `nodeColor` = Color(1.00,0.40,0.40)
  `nodeRad` = 15
  `terminalColors` = [Color(1.00,0.00,0.00), Color(0.00,0.00,1.00), Color(1.00,1.00,0.00), Color(0.00,0.50,0.50), Color(0.00,0.80,0.00), Color(0.50,0.50,0.50), Color(0.80,0.30,0.30), Color(0.30,0.30,0.80), Color(0.80,0.80,0.30), Color(0.30,0.80,0.80)]
  `xOffset` = 20
  `yOffset` = 20