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¶