Coverage for PyRx.dbPlot: 64%

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#$Id: dbPlot.py 170 2013-11-17 21:59:35Z sarkiss $

import wx

from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas

import matplotlib as mpl

import numpy

#----------------------------------------------------------------------

# Taken from FoldPanelBar demo

#----------------------------------------------------------------------

import wx.lib.foldpanelbar as fpb

#import wx.lib.agw.foldpanelbar as fpb

def GetCollapsedIconData():

return'\x89PNG\r\n\x1a\n\x00\x00\x00\rIHDR\x00\x00\x00\x10\x00\x00\x00\x10\x08\x06\

\x00\x00\x00\x1f\xf3\xffa\x00\x00\x00\x04sBIT\x08\x08\x08\x08|\x08d\x88\x00\

\x00\x01\x8eIDAT8\x8d\xa5\x93-n\xe4@\x10\x85?g\x03\n6lh)\xc4\xd2\x12\xc3\x81\

\xd6\xa2I\x90\x154\xb9\x81\x8f1G\xc8\x11\x16\x86\xcd\xa0\x99F\xb3A\x91\xa1\

\xc9J&\x96L"5lX\xcc\x0bl\xf7v\xb2\x7fZ\xa5\x98\xebU\xbdz\xf5\\\x9deW\x9f\xf8\

H\\\xbfO|{y\x9dT\x15P\x04\x01\x01UPUD\x84\xdb/7YZ\x9f\xa5\n\xce\x97aRU\x8a\

\xdc`\xacA\x00\x04P\xf0!0\xf6\x81\xa0\xf0p\xff9\xfb\x85\xe0|\x19&T)K\x8b\x18\

\xf9\xa3\xe4\xbe\xf3\x8c^#\xc9\xd5\n\xa8*\xc5?\x9a\x01\x8a\xd2b\r\x1cN\xc3\

\x14\t\xce\x97a\xb2F0Ks\xd58\xaa\xc6\xc5\xa6\xf7\xdfya\xe7\xbdR\x13M2\xf9\

\xf9qKQ\x1fi\xf6-\x00~T\xfac\x1dq#\x82,\xe5q\x05\x91D\xba@\xefj\xba1\xf0\xdc\

zzW\xcff&\xb8,\x89\xa8@Q\xd6\xaaf\xdfRm,\xee\xb1BDxr#\xae\xf5|\xddo\xd6\xe2H\

\x18\x15\x84\xa0q@]\xe54\x8d\xa3\xedf\x05M\xe3\xd8Uy\xc4\x15\x8d\xf5\xd7\x8b\

~\x82\x0fh\x0e"\xb0\xad,\xee\xb8c\xbb\x18\xe7\x8e;6\xa5\x89\x04\xde\xff\x1c\

\x16\xef\xe0p\xfa>\x19\x11\xca\x8d\x8d\xe0\x93\x1b\x01\xd8m\xf3(;x\xa5\xef=\

\xb7w\xf3\x1d$\x7f\xc1\xe0\xbd\xa7\xeb\xa0(,"Kc\x12\xc1+\xfd\xe8\tI\xee\xed)\

\xbf\xbcN\xc1{D\x04k\x05#\x12\xfd\xf2a\xde[\x81\x87\xbb\xdf\x9cr\x1a\x87\xd3\

0)\xba>\x83\xd5\xb97o\xe0\xaf\x04\xff\x13?\x00\xd2\xfb\xa9`z\xac\x80w\x00\

\x00\x00\x00IEND\xaeB`\x82'

def GetCollapsedIconBitmap():

return wx.BitmapFromImage(GetCollapsedIconImage())

def GetCollapsedIconImage():

import cStringIO

stream = cStringIO.StringIO(GetCollapsedIconData())

return wx.ImageFromStream(stream)

#----------------------------------------------------------------------

def GetExpandedIconData():

return'\x89PNG\r\n\x1a\n\x00\x00\x00\rIHDR\x00\x00\x00\x10\x00\x00\x00\x10\x08\x06\

\x00\x00\x00\x1f\xf3\xffa\x00\x00\x00\x04sBIT\x08\x08\x08\x08|\x08d\x88\x00\

\x00\x01\x9fIDAT8\x8d\x95\x93\xa1\x8e\xdc0\x14EO\xb2\xc4\xd0\xd2\x12\xb7(mI\

\xa4%V\xd1lQT4[4-\x9a\xfe\xc1\xc2|\xc6\xc2~BY\x83:A3E\xd3\xa0*\xa4\xd2\x90H!\

\x95\x0c\r\r\x1fK\x81g\xb2\x99\x84\xb4\x0fY\xd6\xbb\xc7\xf7>=\'Iz\xc3\xbcv\

\xfbn\xb8\x9c\x15 \xe7\xf3\xc7\x0fw\xc9\xbc7\x99\x03\x0e\xfbn0\x99F+\x85R\

\x80RH\x10\x82\x08\xde\x05\x1ef\x90+\xc0\xe1\xd8\ryn\xd0Z-\\A\xb4\xd2\xf7\

\x9e\xfbwoF\xc8\x088\x1c\xbbae\xb3\xe8y&\x9a\xdf\xf5\xbd\xe7\xfem\x84\xa4\

\x97\xccYf\x16\x8d\xdb\xb2a]\xfeX\x18\xc9s\xc3\xe1\x18\xe7\x94\x12cb\xcc\xb5\

\xfa\xb1l8\xf5\x01\xe7\x84\xc7\xb2Y@\xb2\xcc0\x02\xb4\x9a\x88%\xbe\xdc\xb4\

\x9e\xb6Zs\xaa74\xadg[6\x88<\xb7]\xc6\x14\x1dL\x86\xe6\x83\xa0\x81\xba\xda\

\x10\x02x/\xd4\xd5\x06\r\x840!\x9c\x1fM\x92\xf4\x86\x9f\xbf\xfe\x0c\xd6\x9ae\

\xd6u\x8d \xf4\xf5\x165\x9b\x8f\x04\xe1\xc5\xcb\xdb$\x05\x90\xa97@\x04lQas\

\xcd*7\x14\xdb\x9aY\xcb\xb8\\\xe9E\x10|\xbc\xf2^\xb0E\x85\xc95_\x9f\n\xaa/\

\x05\x10\x81\xce\xc9\xa8\xf6><G\xd8\xed\xbbA)X\xd9\x0c\x01\x9a\xc6Q\x14\xd9h\

[\x04\xda\xd6c\xadFkE\xf0\xc2\xab\xd7\xb7\xc9\x08\x00\xf8\xf6\xbd\x1b\x8cQ\

\xd8|\xb9\x0f\xd3\x9a\x8a\xc7\x08\x00\x9f?\xdd%\xde\x07\xda\x93\xc3{\x19C\

\x8a\x9c\x03\x0b8\x17\xe8\x9d\xbf\x02.>\x13\xc0n\xff{PJ\xc5\xfdP\x11""<\xbc\

\xff\x87\xdf\xf8\xbf\xf5\x17FF\xaf\x8f\x8b\xd3\xe6K\x00\x00\x00\x00IEND\xaeB\

`\x82'

def GetExpandedIconBitmap():

return wx.BitmapFromImage(GetExpandedIconImage())

def GetExpandedIconImage():

import cStringIO

stream = cStringIO.StringIO(GetExpandedIconData())

return wx.ImageFromStream(stream)

#----------------------------------------------------------------------

def GetMondrianData():

return'\x89PNG\r\n\x1a\n\x00\x00\x00\rIHDR\x00\x00\x00 \x00\x00\x00 \x08\x06\x00\

\x00\x00szz\xf4\x00\x00\x00\x04sBIT\x08\x08\x08\x08|\x08d\x88\x00\x00\x00qID\

ATX\x85\xed\xd6;\n\x800\x10E\xd1{\xc5\x8d\xb9r\x97\x16\x0b\xad$\x8a\x82:\x16\

o\xda\x84pB2\x1f\x81Fa\x8c\x9c\x08\x04Z{\xcf\xa72\xbcv\xfa\xc5\x08 \x80r\x80\

\xfc\xa2\x0e\x1c\xe4\xba\xfaX\x1d\xd0\xde]S\x07\x02\xd8>\xe1wa-`\x9fQ\xe9\

\x86\x01\x04\x10\x00\\(Dk\x1b-\x04\xdc\x1d\x07\x14\x98;\x0bS\x7f\x7f\xf9\x13\

\x04\x10@\xf9X\xbe\x00\xc9 \x14K\xc1<={\x00\x00\x00\x00IEND\xaeB`\x82'

def GetMondrianBitmap():

return wx.BitmapFromImage(GetMondrianImage())

def GetMondrianImage():

import cStringIO

stream = cStringIO.StringIO(GetMondrianData())

return wx.ImageFromStream(stream)

def GetMondrianIcon():

icon = wx.EmptyIcon()

icon.CopyFromBitmap(GetMondrianBitmap())

return icon

def plotActive(figure, active, inactive):

"Use for a bar plot below"

figure.clf()

axes = figure.add_subplot(121)

axes.cla()

lenActive = len(active)

lenInactive = len(inactive)

if lenActive and lenInactive:

rects1 = axes.bar( numpy.arange(lenActive), active, color='r', edgecolor='r', facecolor ='r' )

rects2 = axes.bar( numpy.arange(lenActive, lenActive + lenInactive), inactive, color='b', edgecolor='b', facecolor='b' )

axes.set_xlim( 0,lenActive + lenInactive )

axes.legend( (rects1[0], rects2[0]), ('Active', 'Inactive') )

axes.set_title("Docking Results")

rocAxes = figure.add_subplot(122)

rocAxes.cla()

#active.extend(inactive)

numArray = numpy.append(active, inactive)

ind = numArray.argsort()

x = []; y =[]

rocAxes.plot([0,1],[0,1], 'b--')

TP = 0.; FP = 0.; lenInd = len(ind)

for i, j in enumerate(ind):

if j >= lenActive:

FP += 1.

else:

TP += 1.

y.append( TP/lenActive )

x.append( FP/lenInactive )

rocAxes.plot(x,y,marker='.')

rocAxes.set_ylabel('True Positive Rate (Sensitivity)')

rocAxes.set_xlabel('False Positive Rate (1 - Specificity)')

rocAxes.set_title("ROC Curve")

return axes

class DBPlotDialog(wx.Dialog):

def __init__( self, parent, useMetal=False,):

# Instead of calling wx.Dialog.__init__ we precreate the dialog

# so we can set an extra style that must be set before

# creation, and then we create the GUI object using the Create

# method.

pre = wx.PreDialog()

pre.SetExtraStyle(wx.DIALOG_EX_CONTEXTHELP)

pre.Create(parent, -1, "Table Plotting Dialog",

size=(350, 200))

# This next step is the most important, it turns this Python

# object into the real wrapper of the dialog (instead of pre)

# as far as the wxPython extension is concerned.

self.PostCreate(pre)

self.parent = parent

# This extra style can be set after the UI object has been created.

if 'wxMac' in wx.PlatformInfo and useMetal:

self.SetExtraStyle(wx.DIALOG_EX_METAL)

# Now continue with the normal construction of the dialog

# contents

sizer = wx.BoxSizer(wx.VERTICAL)

hsizer = wx.BoxSizer(wx.HORIZONTAL)

vsizer = wx.BoxSizer(wx.VERTICAL)

self.tableNames = []

self.updateAxis()

box = wx.StaticBox(self, -1, "Select Table")

bsizer = wx.StaticBoxSizer(box, wx.VERTICAL)

self.tableChoice = wx.Choice(self, -1, (100, 50), choices = self.tableNames)

if 'Docking Results' in self.tableNames:

selection = self.tableNames.index('Docking Results')

else:

selection = 0

self.tableChoice.SetSelection(selection)

self.Bind(wx.EVT_CHOICE, self.EvtTableChoice, self.tableChoice)

bsizer.Add(self.tableChoice, 0, wx.TOP|wx.LEFT, 1)

vsizer.Add(bsizer, 0, wx.EXPAND)

box = wx.StaticBox(self, -1, "Y Column")

bsizer = wx.StaticBoxSizer(box, wx.VERTICAL)

self.yColumnChoice = wx.Choice(self, -1, (100, 50), choices=self.tableYColumns[selection])

self.yColumnChoice.SetSelection(0)

self.Bind(wx.EVT_CHOICE, self.plot, self.yColumnChoice)

bsizer.Add(self.yColumnChoice, 0, wx.TOP|wx.LEFT, 1)

vsizer.Add(bsizer, 0, wx.EXPAND)

#This part is for FoldPanelBar

# self.pnl = fpb.FoldPanelBar(self, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize,

# fpb.FPB_VERTICAL)

# Images = wx.ImageList(16,16)

# Images.Add(GetExpandedIconBitmap())

# Images.Add(GetCollapsedIconBitmap())

# item = self.pnl.AddFoldPanel("More Options", collapsed=True, foldIcons=Images)

# self.pnl.AddFoldPanelWindow(item, wx.StaticText(item, -1, "Add/Subtruct Column"), fpb.FPB_ALIGN_WIDTH, 5, 2)

# self.opChoice = wx.Choice(item, -1, (100, 50), choices = ["None","+","-"])

# self.Bind(wx.EVT_CHOICE, self.plot, self.opChoice)

# self.opChoice.SetSelection(0)

# self.pnl.AddFoldPanelWindow(item, self.opChoice, fpb.FPB_ALIGN_WIDTH, 0, 2)

# self.pnl.AddFoldPanelWindow(item, wx.StaticText(item, -1, "Column:"), fpb.FPB_ALIGN_WIDTH, 0, 2)

# self.opColumnChoice = wx.Choice(item, -1, (100, 50), choices=self.tableYColumns[selection])

# self.opColumnChoice.SetSelection(1)

# self.Bind(wx.EVT_CHOICE, self.plot, self.opColumnChoice)

# self.pnl.AddFoldPanelWindow(item, self.opColumnChoice, fpb.FPB_ALIGN_WIDTH, 0,2)

# vsizer.Add(self.pnl, 1, wx.EXPAND)

hsizer.Add(vsizer, 0, wx.EXPAND)

vsizer = wx.BoxSizer(wx.VERTICAL)

self.figure = mpl.figure.Figure()

self.canvas = Canvas(self, -1, self.figure)

vsizer.Add(self.canvas, 2, wx.EXPAND)

Xsizer = wx.BoxSizer(wx.HORIZONTAL)

box = wx.StaticBox(self, -1, "X Column")

bsizer = wx.StaticBoxSizer(box, wx.VERTICAL)

self.xColumnChoice = wx.Choice(self, -1, (100, 50), choices = self.tableColumns[selection])

self.xColumnChoice.SetSelection(0)

self.Bind(wx.EVT_CHOICE, self.plot, self.xColumnChoice)

bsizer.Add(self.xColumnChoice, 0, wx.TOP|wx.LEFT, 1)

Xsizer.Add(bsizer, 0, wx.EXPAND)

vsizer.Add(Xsizer, 0, wx.EXPAND)

hsizer.Add(vsizer, 1, wx.EXPAND)

sizer.Add(hsizer, 1, wx.EXPAND)

line = wx.StaticLine(self, -1, size=(20,-1), style=wx.LI_HORIZONTAL)

sizer.Add(line, 0, wx.GROW|wx.ALIGN_CENTER_VERTICAL|wx.RIGHT|wx.TOP, 5)

btnsizer = wx.StdDialogButtonSizer()

btn = wx.Button(self, wx.ID_CANCEL)

btnsizer.AddButton(btn)

btn = wx.Button(self, wx.ID_OK)

btn.SetDefault()

btnsizer.AddButton(btn)

btnsizer.Realize()

sizer.Add(btnsizer, 0, wx.ALIGN_RIGHT|wx.ALL, 5)

self.SetSizer(sizer)

sizer.Fit(self)

self.x = None

self.y = None

self.active = None

self.inactive = None

self.title = ""

wx.CallAfter(self.plot)

# def makeAxis(self):

# self.tableNames = []

# for i in range(self.parent.noteBook.GetPageCount()):

# self.tableNames.append(self.parent.noteBook.GetPageText(i))

# self.tableColumns = []

# self.tableYColumns = []

# for index, item in enumerate(self.tableNames):

# columns = []

# yColumns = []

# page = self.parent.noteBook.GetPage(index)

# for i in range(page.list.GetColumnCount()):

# columns.append(page.list.GetColumn(i).Text)

# if page.list.GetColumn(i).Text == "Ligand": continue

# try:

# for value in page.itemDataMap.values():

# float(value[i])

# yColumns.append(page.list.GetColumn(i).Text)

# except:

# pass

# self.tableColumns.append(columns)

# self.tableYColumns.append(yColumns)

def updateAxis(self):

for i in range(self.parent.noteBook.GetPageCount()):

txt = self.parent.noteBook.GetPageText(i)

if not txt in self.tableNames:

if hasattr(self, 'tableChoice'):

self.tableChoice.Append(txt)

self.tableNames.append(txt)

self.tableColumns = []

self.tableYColumns = []

for index, item in enumerate(self.tableNames):

columns = []

yColumns = []

try:

page = self.parent.noteBook.GetPage(index)

if not page:

return

except:

self.tableNames.pop(index)

continue

for i in range(page.list.GetColumnCount()):

columns.append(page.list.GetColumn(i).Text)

if page.list.GetColumn(i).Text == "Ligand": continue

try:

#To make sure that items in y axis are float ir int

for item in page.itemDataMap.values():

float(item[i])

yColumns.append(page.list.GetColumn(i).Text)

except ValueError:

pass

self.tableColumns.append(columns)

self.tableYColumns.append(yColumns)

def EvtTableChoice(self, event):

selection = event.Selection

self.yColumnChoice.SetItems(self.tableYColumns[selection])

for item in self.tableYColumns[selection]:

if item:

self.yColumnChoice.SetStringSelection(item)

break

#self.opColumnChoice.SetItems(self.tableYColumns[selection])

#self.opColumnChoice.SetStringSelection(item)

self.xColumnChoice.SetItems(self.tableColumns[selection])

for item in self.tableColumns[selection]:

if item:

self.xColumnChoice.SetStringSelection(item)

break

self.plot()

event.Skip()

def plot(self, event=None):

self.SetCursor(wx.StockCursor(wx.CURSOR_WAIT))

self.Update()

tableIndex = self.tableChoice.GetSelection()

tablePage = self.parent.noteBook.GetPage(tableIndex)

xIndex = self.xColumnChoice.GetSelection()

yIndex = self.tableColumns[tableIndex].index(self.tableYColumns[tableIndex][self.yColumnChoice.GetSelection()])

x = []

y = []

# op = self.opChoice.GetSelection()

# if op:

# opIndex = self.tableColumns[tableIndex].index(self.tableYColumns[tableIndex][self.opColumnChoice.GetSelection()])

# if op == 1:#+

# opMult = 5

# else:

# opMult = -5

# for value in tablePage.itemDataMap.values():

# x.append(value[xIndex])

# y.append(float(value[yIndex]) +opMult*float(value[opIndex]))

# else:

for value in tablePage.itemDataMap.values():

x.append( value[xIndex] )

y.append(float(value[yIndex]))

if not x:

self.figure.clf()

self.figure.gca().set_title(self.tableNames[tableIndex] + " - "+ self.tableColumns[tableIndex][xIndex]+ " is empty.")

else:

active = []

inactive = []

if len(self.tableNames) > 3 and "PUBCHEM_ACTIVITY_OUTCOME" in self.tableColumns[3] and "results" in tablePage.tableName :

oIndex = self.tableColumns[3].index("PUBCHEM_ACTIVITY_OUTCOME")

cIndex = self.tableColumns[3].index("PUBCHEM_CID")

for item in self.parent.noteBook.GetPage(3).itemDataMap.values():

if item[oIndex] == "Active":

cid = item[cIndex]

try:

active.append(y[x.index(cid)])

except ValueError:

pass

elif item[oIndex] == "Inactive":

cid = item[cIndex]

try:

inactive.append(y[x.index(cid)])

except ValueError:

pass

self.inactive = inactive

self.active = active

if active or inactive:

axes = plotActive( self.figure, active, inactive )

self.title = self.tableNames[tableIndex]+" and ROC Curve"

if not (active or inactive):

self.avtive = None

try:

for i in range( len(x) ):

x[i] = float( x[i] )

except ValueError:

x = numpy.arange(len(x))

if self.tableColumns[tableIndex][xIndex] == "Ligand":

x = numpy.arange(len(x))

self.figure.clf()

axes = self.figure.gca()

#axes.cla()

axes.bar(x, y)

self.x = x

self.y = y

x.sort()

#axes.set_xlim(x[0], x[-1])

self.title = "Table: "+self.tableNames[tableIndex]

axes.set_title(self.title)

yText = self.tableColumns[tableIndex][yIndex]

# if op:

# yText += " " + self.opChoice.GetStringSelection() +" " + self.tableColumns[tableIndex][opIndex]

axes.set_ylabel(yText)

axes.set_xlabel(self.tableColumns[tableIndex][xIndex])

self.axes = axes

self.canvas.draw()

self.SetCursor(wx.NullCursor)

def ShowPlotDialog(parent):

if hasattr(parent,'dlg'):

dlg = parent.dlg

dlg.updateAxis()

dlg.plot(None)

else:

dlg = DBPlotDialog(parent)

parent.dlg = dlg

val = dlg.ShowModal()

if val == wx.ID_OK:

if dlg.x is not None:

if parent.frame.matplot.firstPlot:

parent.frame.matplot.nb.DeletePage(0)

parent.frame.matplot.firstPlot = False

page = parent.frame.matplot.add(dlg.title)

if dlg.active == None:

axes = page.figure.gca()

axes.bar(dlg.x, dlg.y)

dlg.x.sort()

axes.set_xlim(dlg.x[0], dlg.x[-1])

axes.set_title(dlg.figure.gca().get_title())

else:

axes = plotActive( page.figure, dlg.active, dlg.inactive )

axes.set_ylabel(dlg.axes.get_ylabel())

axes.set_xlabel(dlg.axes.get_xlabel())

parent.frame.view.SetSelection(parent.frame.view.GetPageIndex(parent.frame.matplot))

dlg.Show(False)

Coverage for PyRx.dbPlot : 64%

258 statements 165 run 93 missing 0 excluded