def addProbability(self,geoX='',geoY='',data=None,title='',ghost=False,operation='',splitKey='',hue='bfactor',palette='viridis_r',centre=False,vmin=0,vmax=0,categorical=False,restrictions={},exclusions={},range=[]):
isNew = False
if data is None:
isNew = True
gp = geop.GeoPlot(data, geoX, geoY=geoY, title=title, newData=isNew, operation=operation,splitKey=splitKey,
hue=hue,palette=palette,centre=centre,vmin=vmin,vmax=vmax,categorical=categorical,
plot='probability',restrictions=restrictions,exclusions=exclusions,report=self)
gp.range = range
if not ghost:
self.plots.append(gp)
else:
self.plots.append(geop.GeoOverlay(gp, '', title='ghost', report=self))
def addHexBins(self,geoX='',geoY='',data=None,title='',gridsize=50,bins=100,ghost=False,operation='',hue='bfactor',palette='viridis_r',restrictions={},exclusions={},range=[]):
isNew = False
if data is None:
isNew = True
gp = geop.GeoPlot(data, geoX, geoY=geoY, title=title, newData=isNew, operation=operation,
hue=hue,palette=palette,plot='hexbin',restrictions=restrictions,exclusions=exclusions,report=self,gridsize=gridsize)
gp.range = range
if not ghost:
self.plots.append(gp)
else:
self.plots.append(
geop.GeoOverlay(gp, '', title='ghost', report=self))
def addHistogram(self,geoX='',data=None,title='',ghost=False,operation='',splitKey='',hue='DEFAULT',
palette='crimson',count=False,range=[],restrictions={},exclusions={}):
isNew = False
if data is None:
isNew=True
if hue=='':
hue='pdbCode'
gp = geop.GeoPlot(data,geoX,geoY='',title=title,newData=isNew,operation=operation,splitKey=splitKey,
plot='histogram',hue=hue,palette=palette,count=count,restrictions=restrictions,exclusions=exclusions,report=self)
gp.range=range
if not ghost:
self.plots.append(gp)
else:
self.plots.append(geop.GeoOverlay(gp,'',title='ghost',report=self))
return gp
def addSlice(self, slice, palette='viridis', title='',logged=False,centre=False,Contour=True,YellowDots=np.array([])):
gp = geop.GeoPlot(data=None,geoX='',title=title, palette=palette, plot='surface', report=self,centre=centre,Contour=Contour)
gp.surface = slice
gp.logged=logged
gp.differ=0
gp.YellowDots = YellowDots
self.plots.append(gp)
def addSurfaceOverlay(self, surfaces, title='',logged=False):
mat = []
gp = geop.GeoPlot(data=None, geoX='', title=title, plot='surfaces', report=self)
gp.surface = surfaces
gp.logged=logged
self.plots.append(gp)
return mat
def addDifference(self,dataA=None,dataB=None,geoX='',geoY='',restrictionsA={},restrictionsB = {},exclusionsA={},exclusionsB={},title='',palette='seismic'):
isNew = False
if dataA is None:
isNew = True
diffPlot = geop.GeoDifference(dataA=dataA,dataB=dataB,geoX=geoX,geoY=geoY,title=title,
palette=palette,restrictionsA=restrictionsA,restrictionsB=restrictionsB,
exclusionsA=exclusionsA,exclusionsB=exclusionsB,newData=isNew,report=self)
self.plots.append(diffPlot.plotA)
self.plots.append(diffPlot.plotDiff)
self.plots.append(diffPlot.plotB)
def addSlices(self, slices, palette='viridis', title='',logged=False,centre=False,Contour=True):
mat = []
for s in slices:
if mat == []:
mat = s
else:
mat = mat + s
gp = geop.GeoPlot(data=None, geoX='', title=title, palette=palette, plot='surface', report=self,centre=centre,Contour=Contour)
gp.surface = mat
gp.logged=logged
self.plots.append(gp)
return mat
def addCloseContact(self,pdbCode,atomA,atomB,distanceLimit=8.0,ridLimit=2,palette='viridis',hue='distance',categorical=False,title=''):
pdbmanager = geopdb.GeoPdbs(self.pdbDataPath, self.edDataPath, self.ed, self.dssp)
pdb = pdbmanager.getPdb(pdbCode,True)
cc = geocc.CloseContact(pdb,atomA,atomB,distanceLimit,ridLimit,hue)
if hue !='distance':
hue = hue+'A'
df = cc.createContacts()
if title != '':
title += '\n'
title +=atomA+':'+atomB + '\n'
title += 'Max Contact=' + str(distanceLimit) + 'Å\n'
title += 'Residue Gap=' + str(ridLimit)
gp = geop.GeoPlot(data=df, geoX='ridxA', geoY='ridxB', title=title, newData=False, hue=hue,
palette=palette, plot='contact',categorical=categorical,report=self)
self.plots.append(gp)
return df
def addStatsSummary(self, data=None, desc='',geoX='',geoY='', hue='', title=''):
gp = geop.GeoPlot(data, geoX, geoY=geoY, title=title,hue=hue,plot='summary')
gp.descA = desc
self.plots.append(gp)
def addStatsCompare(self, dataA=None, dataB=None, descA='',descB='',geoX='', title=''):
gp = geop.GeoPlot(dataA, geoX, title=title,plot='compare')
gp.data2 = dataB
gp.descA = descA
gp.descB = descB
self.plots.append(gp)
def addComment(self, comment):
gp = geop.GeoPlot(data=pd.DataFrame(),title=comment,plot='comment',geoX='')
self.plots.append(gp)
def addCsv(self, data, title=''):
gp = geop.GeoPlot(data=data,title=title,plot='csv',geoX='')
self.plots.append(gp)