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