def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self,text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
label = Label(eframe,text="Pipeline:")#,fg=textLightColor,bg=baseColor)
label.grid(row=3,column=0,sticky=W,padx=10,pady=5)
Pipelines=["InitialChIPseqQC", "ChIPseq" ]
Pipeline = self.Pipeline = StringVar()
Pipeline.set(Pipelines[0])
om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
om.config()#bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3,column=1,sticky=W,padx=20,pady=5)
#readtypes = ['Single', 'Paired']
#self.readtype = readtype = StringVar()
#readtype.set(readtypes[0])
#readtype_menu = OptionMenu(eframe, readtype, *readtypes)
#readtype_menu.grid(row=3, column=3, sticky=E, pady=5)
#readtype_label = Label(eframe, text="-end ")
#readtype_label.grid( row=3, column=4, stick=W, pady=5)
self.add_info(eframe)
self.option_controller()
self.peakinfo_fn = 'peakcall.tab'
self.contrast_fn = 'contrast.tab'
def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.pairs = None
eframe = self.eframe = LabelFrame(self, text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)
label = Label(eframe,
text="Pipeline") #,fg=textLightColor,bg=baseColor)
label.grid(row=3, column=0, sticky=W, padx=10, pady=5)
PipelineLabels = [
'Initial QC', 'Germline', 'Somatic Tumor-Normal',
'Somatic Tumor-Only'
]
Pipelines = [
"initialqcgenomeseq", "wgslow", 'wgs-somatic',
'wgs-somatic-tumoronly'
]
self.label2pipeline = {k: v for k, v in zip(PipelineLabels, Pipelines)}
PipelineLabel = self.PipelineLabel = StringVar()
Pipeline = self.Pipeline = StringVar()
PipelineLabel.set(PipelineLabels[0])
#om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
om = OptionMenu(eframe,
PipelineLabel,
*PipelineLabels,
command=self.option_controller)
om.config() #bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config() #bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3, column=1, sticky=W, padx=10, pady=5)
def option_controller( self, *args, **kwargs ) :
PipelineFrame.option_controller( self )
self.Pipeline.set( self.label2pipeline[self.PipelineLabel.get()] )
print( self.Pipeline.get() )
if self.Pipeline.get() == 'cellranger' :
self.clusterOpts.grid_forget()
self.crOpts.grid(row=8,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
self.qcOpts.grid_forget()
self.multiclusterOpts.grid_forget()
elif self.Pipeline.get() == 'scrnaseqcluster' :
self.clusterOpts.grid( row=8, column=0, columnspan=4, sticky=W, padx=20, pady=10 )
self.crOpts.grid_forget()
self.qcOpts.grid_forget()
self.multiclusterOpts.grid_forget()
elif self.Pipeline.get() == 'scrnaseqinit' :
self.clusterOpts.grid_forget()
self.crOpts.grid_forget()
self.qcOpts.grid( row=8, column=0, columnspan=4, sticky=W, padx=20, pady=10 )
self.multiclusterOpts.grid_forget()
elif self.Pipeline.get() == 'scrnaseqmulticluster' :
self.clusterOpts.grid_forget()
self.crOpts.grid_forget()
self.qcOpts.grid_forget()
self.multiclusterOpts.grid( row=8, column=0, columnspan=4, sticky=W, padx=20, pady=10 )
def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self, text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)
label = Label(eframe,
text="Pipeline") #,fg=textLightColor,bg=baseColor)
label.grid(row=3, column=0, sticky=W, padx=10, pady=5)
Pipelines = ["CAPmirseq-plus"]
Pipeline = self.Pipeline = StringVar()
Pipeline.set(Pipelines[0])
om = OptionMenu(eframe,
Pipeline,
*Pipelines,
command=self.option_controller)
om.config() #bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config() #bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3, column=1, sticky=W, padx=10, pady=5)
self.add_info(eframe)
def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self,text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
label = Label(eframe,text="Pipeline:")#,fg=textLightColor,bg=baseColor)
label.grid(row=3,column=0,sticky=W,padx=10,pady=5)
Pipelines=["InitialChIPseqQC", "ChIPseq" ]
Pipeline = self.Pipeline = StringVar()
Pipeline.set(Pipelines[0])
om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
om.config()#bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3,column=1,sticky=W,padx=20,pady=5)
readtypes = ['Single', 'Paired']
self.readtype = readtype = StringVar()
readtype.set(readtypes[0])
readtype_menu = OptionMenu(eframe, readtype, *readtypes)
readtype_menu.grid(row=3, column=3, sticky=E, pady=5)
readtype_label = Label(eframe, text="-end ")
readtype_label.grid( row=3, column=4, stick=W, pady=5)
self.add_info(eframe)
self.option_controller()
self.peakinfo_fn = 'peakcall.tab'
self.contrast_fn = 'contrast.tab'
def option_controller(self, *args, **kwargs):
PipelineFrame.option_controller(self)
self.Pipeline.set(self.label2pipeline[self.PipelineLabel.get()])
print(self.Pipeline.get())
if self.Pipeline.get() == 'initialqcrnaseq':
self.om4.grid_forget()
self.sampleLF.grid_forget()
self.info.grid_forget()
elif self.Pipeline.get() == 'rnaseq':
self.om4.grid(row=6, column=1, sticky=W, padx=10, pady=5)
self.sampleLF.grid(row=8,
column=0,
columnspan=4,
sticky=W,
padx=20,
pady=10)
self.info.grid(row=10,
column=0,
columnspan=6,
sticky=W,
padx=20,
pady=10)
else:
self.om4.grid_forget()
self.sampleLF.grid_forget()
self.info.grid_forget()
def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.pairs = None
eframe = self.eframe = LabelFrame(self,text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
label = Label(eframe,text="Pipeline")#,fg=textLightColor,bg=baseColor)
label.grid(row=3,column=0,sticky=W,padx=10,pady=5)
PipelineLabels = ['Initial QC',
'Germline',
'Somatic Tumor-Normal',
'Somatic Tumor-Only']
Pipelines=["initialqcgenomeseq",
"wgslow",
'wgs-somatic',
'wgs-somatic-tumoronly']
self.label2pipeline = { k:v for k,v in zip(PipelineLabels, Pipelines)}
PipelineLabel = self.PipelineLabel = StringVar()
Pipeline = self.Pipeline = StringVar()
PipelineLabel.set(PipelineLabels[0])
#om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
om = OptionMenu(eframe, PipelineLabel, *PipelineLabels, command=self.option_controller)
om.config()#bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3,column=1,sticky=W,padx=10,pady=5)
def option_controller( self, *args, **kwargs ) :
PipelineFrame.option_controller( self )
if self.Pipeline.get() == 'exomeseq-somatic' :
self.add_pairs( self.eframe )
#self.dry_button.config( state="disabled" )
elif self.Pipeline.get() != 'exomeseq-somatic' :
self.del_pairs( self.eframe )
def option_controller(self, *args, **kwargs):
PipelineFrame.option_controller(self)
self.Pipeline.set(self.label2pipeline[self.PipelineLabel.get()])
print(self.Pipeline.get())
if self.Pipeline.get() == 'exomeseq-somatic':
self.add_pairs(self.eframe)
#self.dry_button.config( state="disabled" )
elif self.Pipeline.get() != 'exomeseq-somatic':
self.del_pairs(self.eframe)
def option_controller( self, *args, **kwargs ) :
PipelineFrame.option_controller( self )
self.Pipeline.set( self.label2pipeline[self.PipelineLabel.get()] )
print( self.Pipeline.get() )
if self.Pipeline.get() == 'wgs-somatic' :
self.add_pairs( self.eframe )
#self.dry_button.config( state="disabled" )
elif self.Pipeline.get() != 'wgs-somatic' :
self.del_pairs( self.eframe )
def option_controller(self, *args, **kwargs):
PipelineFrame.option_controller(self)
if self.Pipeline.get() == 'InitialChIPseqQC':
self.info.grid_forget()
else:
self.info.grid(row=7,
column=0,
columnspan=6,
sticky=W,
padx=20,
pady=10)
def option_controller(self, *args, **kwargs):
PipelineFrame.option_controller(self)
if self.Pipeline.get() == 'initialqcrnaseq':
self.om4.grid_forget()
self.sampleLF.grid_forget()
else:
self.om4.grid(row=6, column=1, sticky=W, padx=10, pady=5)
self.sampleLF.grid(row=8,
column=0,
columnspan=4,
sticky=W,
padx=20,
pady=10)
def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.pairs = None
eframe = self.eframe = LabelFrame(self,text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
label = Label(eframe,text="Pipeline")#,fg=textLightColor,bg=baseColor)
label.grid(row=3,column=0,sticky=W,padx=10,pady=5)
PipelineLabels = ["Initial QC", "Germline", 'Somatic Tumor-Normal', 'Somatic Tumor-Only']
Pipelines=["initialqc", "exomeseq-germline", "exomeseq-somatic", "exomeseq-somatic-tumoronly"]
self.label2pipeline = { k:v for k,v in zip(PipelineLabels, Pipelines)}
Pipeline = self.Pipeline = StringVar()
PipelineLabel = self.PipelineLabel = StringVar()
self.Pipeline = StringVar()
PipelineLabel.set(PipelineLabels[0])
om = OptionMenu(eframe, PipelineLabel, *PipelineLabels, command=self.option_controller)
#om.config()#bg = widgetBgColor,fg=widgetFgColor)
#om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3,column=1,sticky=W,padx=10,pady=5)
targetsL=Label(eframe,
text="Target Capture Kit")
#,fg=textLightColor,bg=baseColor)
targetsL.grid(row=5,column=0,sticky=W,padx=10,pady=5)
targetsE = Entry(eframe,textvariable=self.targetspath, width=50)
if self.genome=="hg19":
self.targetspath.set(
"/data/CCBR_Pipeliner/db/PipeDB/lib/SS_v5_UTRs_hg19.bed" )
elif self.genome=="hg38":
self.targetspath.set(
"/data/CCBR_Pipeliner/db/PipeDB/lib/SS_v5_UTRs_hg38.bed" )
else:
self.targetspath.set(
"/data/CCBR_Pipeliner/db/PipeDB/lib/SureSelect_mm10.bed")
targetsE.grid(row=5,column=1,columnspan=6,sticky=W,padx=10,pady=5)
self.targetspath.trace('w', lambda a,b,c,x="targetspath":self.makejson(x))
label = Label (eframe,
text =
"By default, the path to the Agilent V5+UTR targets file is filled in here" )
label.grid(row=6, column=0, columnspan=5, sticky=W, padx=10, pady=5)
def option_controller(self, *args, **kwargs):
PipelineFrame.option_controller(self)
self.Pipeline.set(self.label2pipeline[self.PipelineLabel.get()])
print(self.Pipeline.get())
if self.Pipeline.get() == 'miRSeq_v2':
self.novelMirsFrame.grid(row=5,
column=0,
columnspan=4,
sticky=W,
padx=20,
pady=10)
elif self.Pipeline.get() == "CAPmirseq-plus":
self.novelMirsFrame.grid_forget()
def option_controller(self, *args, **kwargs):
PipelineFrame.option_controller(self)
self.Pipeline.set(self.label2pipeline[self.PipelineLabel.get()])
print(self.Pipeline.get())
if self.Pipeline.get() == 'cellranger':
self.clusterOpts.grid_forget()
self.crOpts.grid(row=8,
column=0,
columnspan=6,
sticky=W,
padx=20,
pady=10)
self.qcOpts.grid_forget()
self.multiclusterOpts.grid_forget()
elif self.Pipeline.get() == 'scrnaseqcluster':
self.clusterOpts.grid(row=8,
column=0,
columnspan=4,
sticky=W,
padx=20,
pady=10)
self.crOpts.grid_forget()
self.qcOpts.grid_forget()
self.multiclusterOpts.grid_forget()
elif self.Pipeline.get() == 'scrnaseqinit':
self.clusterOpts.grid_forget()
self.crOpts.grid_forget()
self.qcOpts.grid(row=8,
column=0,
columnspan=4,
sticky=W,
padx=20,
pady=10)
self.multiclusterOpts.grid_forget()
elif self.Pipeline.get() == 'scrnaseqmulticluster':
self.clusterOpts.grid_forget()
self.crOpts.grid_forget()
self.qcOpts.grid_forget()
self.multiclusterOpts.grid(row=8,
column=0,
columnspan=4,
sticky=W,
padx=20,
pady=10)
def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.pairs = None
eframe = self.eframe = LabelFrame(self,text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
label = Label(eframe,text="Pipeline")#,fg=textLightColor,bg=baseColor)
label.grid(row=3,column=0,sticky=W,padx=10,pady=5)
Pipelines=["initialqcgenomeseq","wgslow"]
Pipeline = self.Pipeline = StringVar()
Pipeline.set(Pipelines[0])
om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
om.config()#bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3,column=1,sticky=W,padx=10,pady=5)
def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self, text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)
label = Label(eframe,
text="Pipeline") #,fg=textLightColor,bg=baseColor)
label.grid(row=3, column=0, sticky=W, padx=10, pady=5)
PipelineLabels = ["miRSeq_v2", "CAPmirseq-plus"]
Pipelines = ["miRSeq_v2", "CAPmirseq-plus"]
self.label2pipeline = {k: v for k, v in zip(PipelineLabels, Pipelines)}
PipelineLabel = self.PipelineLabel = StringVar()
Pipeline = self.Pipeline = StringVar()
PipelineLabel.set(PipelineLabels[0])
om = OptionMenu(eframe,
PipelineLabel,
*PipelineLabels,
command=self.option_controller)
om.config() #bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config() #bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3, column=1, sticky=W, padx=10, pady=5)
# self.mirseqOpts = mirseqOpts = LabelFrame(eframe,text="miRSeq Settings")
self.novelMirsFrame = novelMirsFrame = Frame(eframe)
self.novelMirs = novelMirs = StringVar()
novelMirLabel = Label(novelMirsFrame, text="Identify Novel miRNAs: ")
novelMirsDropdown = ["YES", "NO"]
novelMirs.set(novelMirsDropdown[1])
novelMirs_om = OptionMenu(novelMirsFrame, novelMirs,
*novelMirsDropdown)
novelMirLabel.grid(row=5, column=1, sticky=W, padx=10, pady=5)
novelMirs_om.grid(row=5, column=2, sticky=W, padx=10, pady=0)
# novelMirsFrame.grid(row=5,column=0, columnspan=4, sticky=W, padx=20, pady=10 )
self.add_info(eframe)
self.option_controller()
def option_controller(self, *args, **kwargs):
PipelineFrame.option_controller(self)
if self.Pipeline.get() == 'InitialChIPseqQC':
self.info.grid_forget()
self.om_peaks.grid(row=7,
column=0,
columnspan=6,
sticky=W,
padx=20,
pady=10)
elif self.Pipeline.get() == 'ChIPseq':
self.info.grid(row=7,
column=0,
columnspan=6,
sticky=W,
padx=20,
pady=10)
contrast_file = join(self.workpath.get(), self.contrast_fn)
print(contrast_file)
if not os.path.exists(contrast_file):
open(contrast_file, 'a').close()
def option_controller(self, *args, **kwargs):
PipelineFrame.option_controller(self)
self.Pipeline.set(self.label2pipeline[self.PipelineLabel.get()])
print(self.Pipeline.get())
if self.Pipeline.get() == 'scrnaQC':
self.deOptions.grid_forget()
self.qcOptions.grid(row=8,
column=0,
columnspan=6,
sticky=W,
padx=20,
pady=10)
elif self.Pipeline.get() == 'scrnaDE':
self.deOptions.grid(row=8,
column=0,
columnspan=4,
sticky=W,
padx=20,
pady=10)
self.qcOptions.grid_forget()
def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self, text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)
label = Label(eframe,
text="Pipeline") #,fg=textLightColor,bg=baseColor)
label.grid(row=3, column=0, sticky=W, padx=10, pady=5)
PipelineLabels = [
"CellRanger", "Initial/QC", "Clustering", "Multi-Sample Clustering"
]
Pipelines = [
"cellranger", "scrnaseqinit", "scrnaseqcluster",
"scrnaseqmulticluster"
]
self.label2pipeline = {k: v for k, v in zip(PipelineLabels, Pipelines)}
PipelineLabel = self.PipelineLabel = StringVar()
self.Pipeline = StringVar()
PipelineLabel.set(PipelineLabels[0])
om = OptionMenu(eframe,
PipelineLabel,
*PipelineLabels,
command=self.option_controller)
om.config() #bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config() #bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3, column=1, sticky=W, padx=10, pady=5)
self.crOpts = crOpts = LabelFrame(eframe, text="CellRanger Settings")
self.scrCRID = scrCRID = StringVar()
scrCRID.set("SPECIFY_PREFIX_HERE")
self.scrExpected = scrExpected = StringVar()
scrExpected.set("3000")
scrcridL = Label(crOpts, text="CellRanger Sample ID: ")
scrcridE = Entry(crOpts, bd=2, width=25, textvariable=scrCRID)
scrcridL.grid(row=9, column=1, sticky=W, padx=10, pady=5)
scrcridE.grid(row=9, column=2, sticky=W, padx=0, pady=5)
screxpectedL = Label(crOpts, text="Expected number of cells: ")
screxpectedE = Entry(crOpts, bd=2, width=8, textvariable=scrExpected)
screxpectedL.grid(row=10, column=1, sticky=W, padx=10, pady=5)
screxpectedE.grid(row=10, column=2, sticky=W, padx=0, pady=5)
self.clusterOpts = clusterOpts = LabelFrame(
eframe, text="Clustering and tSNE Options")
self.scrPCs = scrPCs = StringVar()
scrPCs.set("12")
self.scrRes = scrRes = StringVar()
scrRes.set("0.6")
#scrPCs.trace('w', lambda a,b,c,x="scrPCs": makejson(x))
#Filter out genes < [5] read counts in < [2] samples
scrpcsL = Label(clusterOpts,
text="Include principal components 1 through ")
scrpcsE = Entry(clusterOpts, bd=2, width=3, textvariable=scrPCs)
scrresL = Label(clusterOpts, text="with clustering resolution: ")
scrresE = Entry(clusterOpts, bd=2, width=3, textvariable=scrRes)
scrpcsL.grid(row=9, column=1, sticky=W, padx=10, pady=5)
scrpcsE.grid(row=9, column=2, sticky=W, padx=0, pady=5)
scrresL.grid(row=9, column=3, sticky=W, padx=5, pady=5)
scrresE.grid(row=9, column=4, sticky=W, padx=0, pady=5)
#scrRes.trace('w', lambda a,b,c,x="scrPCs": makejson(x))
clusterOpts.grid(row=8,
column=0,
columnspan=4,
sticky=W,
padx=20,
pady=10)
self.multiclusterOpts = multiclusterOpts = LabelFrame(
eframe, text="Multi-Sample Clustering and tSNE Options")
scrccsL = Label(multiclusterOpts,
text="Include canonical components 1 through ")
scrccsE = Entry(multiclusterOpts, bd=2, width=3, textvariable=scrPCs)
scrmcresL = Label(multiclusterOpts,
text="with clustering resolution: ")
scrmcresE = Entry(multiclusterOpts, bd=2, width=3, textvariable=scrRes)
scrccsL.grid(row=9, column=1, sticky=W, padx=10, pady=5)
scrccsE.grid(row=9, column=2, sticky=W, padx=0, pady=5)
scrmcresL.grid(row=9, column=3, sticky=W, padx=5, pady=5)
scrmcresE.grid(row=9, column=4, sticky=W, padx=0, pady=5)
self.qcOpts = qcOpts = LabelFrame(eframe, text="Initial Settings")
countL = Label(qcOpts, text="Counts/Matrix Dir:")
countL.grid(row=9, column=1, sticky=W, padx=10, pady=5)
countpath = StringVar()
self.countpath = countpath
count_entry = Entry(
qcOpts,
bd=2,
width=50,
#bg = entryBgColor,
#fg = entryFgColor,
textvariable=countpath,
state='normal')
count_entry.grid(row=9, column=2, columnspan=3)
self.count_button = count_button = Button(
qcOpts, text="Open Directory", command=self.set_count_directory)
count_button.grid(row=9, column=5)
self.mattype = mattype = StringVar()
mattypeL = Label(qcOpts, text="Count matrix format: ")
scrMatTypeDropdown = ["cellranger", "cellranger_raw", "zumi", "biorad"]
mattype.set(scrMatTypeDropdown[0])
mattype_om = OptionMenu(qcOpts, mattype, *scrMatTypeDropdown)
mattypeL.grid(row=10, column=1, sticky=W, padx=10, pady=5)
mattype_om.grid(row=10, column=2, sticky=W, padx=0, pady=5)
self.docycleregress = docycleregress = StringVar()
docycleregressL = Label(qcOpts, text="Do cell cycle regression? ")
scrCycleDropdown = ["TRUE", "FALSE"]
docycleregress.set(scrCycleDropdown[0])
cycle_om = OptionMenu(qcOpts, docycleregress, *scrCycleDropdown)
docycleregressL.grid(row=11, column=1, sticky=W, padx=10, pady=5)
cycle_om.grid(row=11, column=2, sticky=W, padx=0, pady=5)
usecycleregressL_c = Label(clusterOpts,
text="Use cell cycle regressed data? ")
docycleregress.set(scrCycleDropdown[0])
cycle_om_c = OptionMenu(clusterOpts, docycleregress, *scrCycleDropdown)
usecycleregressL_c.grid(row=10, column=1, sticky=W, padx=10, pady=5)
cycle_om_c.grid(row=10, column=2, sticky=W, padx=0, pady=5)
usecycleregressL_mc = Label(multiclusterOpts,
text="Use cell cycle regressed data? ")
docycleregress.set(scrCycleDropdown[0])
cycle_om_mc = OptionMenu(multiclusterOpts, docycleregress,
*scrCycleDropdown)
usecycleregressL_mc.grid(row=10, column=1, sticky=W, padx=10, pady=5)
cycle_om_mc.grid(row=10, column=2, sticky=W, padx=0, pady=5)
groups_buttonL = Label(qcOpts, text="SAMPLE INFORMATION: ")
groups_button = Button(qcOpts,
text="Set Groups",
command=self.popup_groups)
groups_buttonL.grid(row=12, column=1, sticky=W, padx=10, pady=5)
groups_button.grid(row=12, column=2, sticky=W, padx=0, pady=5)
#####################
self.option_controller()
def popup_window( self, title, filename, kind='textbox' ) :
if kind == 'textbox' :
PipelineFrame.popup_window(self, title, filename)
elif kind == 'peakinfo' :
self.popup_window_peakinfo(title, filename)
def option_controller( self, *args, **kwargs ) :
PipelineFrame.option_controller( self )
if self.Pipeline.get() == 'InitialChIPseqQC' :
self.info.grid_forget()
else :
self.info.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
def popup_window(self, title, filename, kind='textbox'):
if kind == 'textbox':
PipelineFrame.popup_window(self, title, filename)
elif kind == 'peakinfo':
self.popup_window_peakinfo(title, filename)
def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self, text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)
label = Label(eframe,
text="Pipeline") #,fg=textLightColor,bg=baseColor)
label.grid(row=3, column=0, sticky=W, padx=10, pady=5)
PipelineLabels = ["Initial QC", "Differential Expression"]
Pipelines = ["scrnaQC", "scrnaDE"]
self.label2pipeline = {k: v for k, v in zip(PipelineLabels, Pipelines)}
PipelineLabel = self.PipelineLabel = StringVar()
self.Pipeline = StringVar()
PipelineLabel.set(PipelineLabels[0])
om = OptionMenu(eframe,
PipelineLabel,
*PipelineLabels,
command=self.option_controller)
om.config() #bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config() #bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3, column=1, sticky=W, padx=10, pady=5)
######## QUALITY CONTROL/FILTERING/CLUSTERING ###############
self.qcOptions = qcOptions = LabelFrame(
eframe, text="QC, Filtering, and Initial Clustering")
#algorithm selection
self.clustAlg = clustAlg = StringVar()
clustAlgLabel = Label(qcOptions, text="Clustering Algorithm: ")
clustAlgDropdown = [
"SLM (Smart Local Moving)", "Louvain (Original)",
"Louvain (with Multilevel Refinement)"
]
clustAlg.set(clustAlgDropdown[0])
clustAlgOptMenu = OptionMenu(qcOptions, clustAlg, *clustAlgDropdown)
clustAlgLabel.grid(row=8, column=1, sticky=W, padx=10, pady=5)
clustAlgOptMenu.grid(row=8, column=2, sticky=W, padx=0, pady=5)
#clustering resolutions
self.resolution = resolution = StringVar()
resolution.set("0.4,0.6,0.8,1.0,1.2")
resolutionLabel = Label(
qcOptions, text="Clustering Resolution(s): \nSeparate with commas")
resolutionEntry = Entry(qcOptions,
bd=2,
width=25,
textvariable=resolution)
resolutionLabel.grid(row=9, column=1, sticky=W, padx=10, pady=5)
resolutionEntry.grid(row=9, column=2, sticky=W, padx=0, pady=5)
#annotation db: human: HPCA/BP Encode; mouse: immgen/mouseRNAseq
self.annotDB = annotDB = StringVar()
annotLabel = Label(qcOptions, text="Annotation database: ")
annotHuman = [
"Human Primary Cell Atlas", "Blueprint/ENCODE", "Monaco Immune",
"Database of Immune Cell Expression (DICE)"
]
annotMouse = ["ImmGen", "Mouse RNASeq"]
annotDropdown = []
genome = self.global_info.annotation.get()
if (genome == "GRCh38"):
annotDropdown = annotHuman.copy()
elif (genome == "mm10"):
annotDropdown = annotMouse.copy()
else:
annotDropdown.append("No genome selected")
annotDB.set(annotDropdown[0])
annotDB_om = OptionMenu(qcOptions, annotDB, *annotDropdown)
annotLabel.grid(row=10, column=1, sticky=W, padx=10, pady=5)
annotDB_om.grid(row=10, column=2, sticky=W, padx=0, pady=5)
self.citeseq = citeseq = StringVar()
citeseqLabel = Label(qcOptions, text="CITESeq Included: ")
citeseqDropdown = ["Yes", "No"]
citeseq.set(citeseqDropdown[1])
citeseqOptMenu = OptionMenu(qcOptions, citeseq, *citeseqDropdown)
citeseqLabel.grid(row=11, column=1, sticky=W, padx=10, pady=5)
citeseqOptMenu.grid(row=11, column=2, sticky=W, padx=0, pady=5)
#set groups, mostly for relabeling purposes
self.add_info(qcOptions) #Position 13
# self.option_controller()
# groups_buttonL = Label(qcOptions, text="Sample Information: ")
# groups_button = Button(qcOptions,
# text="Set Groups",
# command = self.popup_groups )
# groups_buttonL.grid(row=12,column=1,sticky=W,padx=10,pady=5)
# groups_button.grid(row=12,column=2,sticky=W,padx=0,pady=5)
#
#
######### DIFFERENTIAL EXPRESSION #########
self.deOptions = deOptions = LabelFrame(
eframe, text="Differential Gene Expression")
#option for which object to run DE on
self.rdsObject = rdsObject = StringVar()
rdsLabel = Label(deOptions,
text="Use the pre- or post-batch corrected data:")
rdsDropdown = [
"Merged (Pre-batch correction)",
"Integrated (Post-batch correction)", "Both"
]
rdsObject.set(rdsDropdown[2])
rdsOptMenu = OptionMenu(deOptions, rdsObject, *rdsDropdown)
rdsLabel.grid(row=8, column=1, sticky=W, padx=10, pady=5)
rdsOptMenu.grid(row=8, column=2, sticky=W, padx=0, pady=5)
#option for cluster resolution for DE
self.resolutionDE = resolutionDE = StringVar()
resolutionDE.set("0.4,0.6,0.8,1.0,1.2")
resolutionDELabel = Label(
deOptions,
text=
"Clustering Resolution: \nChoose a previous resolution or \nselect a new resolution to run"
)
resolutionDEEntry = Entry(deOptions,
bd=2,
width=25,
textvariable=resolutionDE)
resolutionDELabel.grid(row=9, column=1, sticky=W, padx=10, pady=5)
resolutionDEEntry.grid(row=9, column=2, sticky=W, padx=0, pady=5)
#options for difftest
self.testDE = testDE = StringVar()
testDELabel = Label(
deOptions, text="Statistical test for differential expression:")
testDEDropdown = [
"MAST", "DESeq2", "Likelihood Ratio", "Logistic regression",
"Negative Binomial", "Wilcoxon", "Student's T"
]
testDE.set(testDEDropdown[0])
testDEMenu = OptionMenu(deOptions, testDE, *testDEDropdown)
testDELabel.grid(row=10, column=1, sticky=W, padx=10, pady=5)
testDEMenu.grid(row=10, column=2, sticky=W, padx=0, pady=5)
#options for filters
self.deMinPct = deMinPct = StringVar()
deMinPctLabel = Label(
deOptions, text="Minimum fraction of cells expressing DE genes:")
deMinPct.set("0.1")
deMinPctEntry = Entry(deOptions, bd=2, width=10, textvariable=deMinPct)
deMinPctLabel.grid(row=11, column=1, sticky=W, padx=10, pady=5)
deMinPctEntry.grid(row=11, column=2, sticky=W, padx=0, pady=5)
self.deMinFC = deMinFC = StringVar()
deMinFCLabel = Label(deOptions,
text="Minimum fold change to report DE genes:")
deMinFC.set("0.25")
deMinFCEntry = Entry(deOptions, bd=2, width=10, textvariable=deMinFC)
deMinFCLabel.grid(row=12, column=1, sticky=W, padx=10, pady=5)
deMinFCEntry.grid(row=12, column=2, sticky=W, padx=0, pady=5)
#use groups and contrasts for differential expression, have options to create new groups
self.om_groups = LabelFrame(deOptions, text="Sample Information")
self.groups_button = Button(self.om_groups,
text="Set Groups",
command=self.popup_groups)
self.groups_button.grid(row=5, column=5, padx=10, pady=5)
self.contrasts_button = Button(self.om_groups,
text="Set Contrasts",
command=self.popup_groups)
self.contrasts_button.grid(row=5, column=6, padx=10, pady=5)
self.om_groups.grid(row=13,
column=0,
columnspan=6,
sticky=W,
padx=20,
pady=10)
#option for merged/integrated object
# self.integrateOption = integrateOption = StringVar()
# integrateLabel = Label(deOptions, text="Merged or Integrated (batch corrected): ")
# integrateDropdown = ["Merged","Integrated"]
# integrateOption.set(integrateDropdown[0])
# integrateOptMenu = OptionMenu(deOptions, integrateOption, *integrateDropdown)
# integrateLabel.grid(row=9,column=1,sticky=W,padx=10,pady=5)
# integrateOptMenu.grid(row=9,column=2,sticky=W,padx=0,pady=5)
self.option_controller()
def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self,text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
label = Label(eframe,text="Pipeline")#,fg=textLightColor,bg=baseColor)
label.grid(row=3,column=0,sticky=W,padx=10,pady=5)
PipelineLabels=["CellRanger","Initial/QC","Clustering" ]
Pipelines=["cellranger","scrnaseqinit","scrnaseqcluster"]
self.label2pipeline = { k:v for k,v in zip(PipelineLabels, Pipelines)}
PipelineLabel = self.PipelineLabel = StringVar()
self.Pipeline = StringVar()
PipelineLabel.set(PipelineLabels[0])
om = OptionMenu(eframe, PipelineLabel, *PipelineLabels, command=self.option_controller)
om.config()#bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3,column=1,sticky=W,padx=10,pady=5)
self.crOpts = crOpts = LabelFrame( eframe,
text="CellRanger Settings" )
self.scrCRID = scrCRID = StringVar()
scrCRID.set("SPECIFY_PREFIX_HERE")
self.scrExpected = scrExpected = StringVar()
scrExpected.set("3000")
scrcridL = Label(crOpts, text="CellRanger Sample ID: ")
scrcridE = Entry(crOpts, bd =2, width=25, textvariable=scrCRID)
scrcridL.grid(row=9,column=1,sticky=W,padx=10,pady=5)
scrcridE.grid(row=9,column=2,sticky=W,padx=0,pady=5)
screxpectedL = Label(crOpts, text="Expected number of cells: ")
screxpectedE = Entry(crOpts, bd =2, width=8, textvariable=scrExpected)
screxpectedL.grid(row=10,column=1,sticky=W,padx=10,pady=5)
screxpectedE.grid(row=10,column=2,sticky=W,padx=0,pady=5)
self.clusterOpts = clusterOpts = LabelFrame( eframe,
text="Clustering and tSNE Options" )
self.scrPCs = scrPCs = StringVar()
scrPCs.set("12")
self.scrRes = scrRes = StringVar()
scrRes.set("0.6")
#scrPCs.trace('w', lambda a,b,c,x="scrPCs": makejson(x))
#Filter out genes < [5] read counts in < [2] samples
scrpcsL = Label(clusterOpts, text="Include principal components 1 through ")
scrpcsE = Entry(clusterOpts, bd =2, width=3, textvariable=scrPCs)
scrresL = Label(clusterOpts, text="with clustering resolution: ")
scrresE = Entry(clusterOpts, bd =2, width=3, textvariable=scrRes)
scrpcsL.grid(row=9,column=1,sticky=W,padx=10,pady=5)
scrpcsE.grid(row=9,column=2,sticky=W,padx=0,pady=5)
scrresL.grid(row=9,column=3,sticky=W,padx=5,pady=5)
scrresE.grid(row=9,column=4,sticky=W,padx=0,pady=5)
#scrRes.trace('w', lambda a,b,c,x="scrPCs": makejson(x))
clusterOpts.grid( row=8, column=0, columnspan=4, sticky=W, padx=20, pady=10 )
self.qcOpts = qcOpts = LabelFrame( eframe,
text="Initial Settings" )
countL = Label( qcOpts, text="Counts/Matrix Dir:" )
countL.grid(row=9, column=1, sticky=W, padx=10, pady=5 )
countpath=StringVar()
self.countpath = countpath
count_entry = Entry(qcOpts,
bd =2,
width = 50,
#bg = entryBgColor,
#fg = entryFgColor,
textvariable = countpath, state='normal'
)
count_entry.grid( row=9, column=2, columnspan=3 )
self.count_button = count_button = Button( qcOpts,
text="Open Directory",
command=self.set_count_directory )
count_button.grid( row=9, column=5 )
#####################
self.option_controller()
def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.pairs = None
eframe = self.eframe = LabelFrame(self, text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)
label = Label(eframe,
text="Pipeline") #,fg=textLightColor,bg=baseColor)
label.grid(row=3, column=0, sticky=W, padx=10, pady=5)
PipelineLabels = [
"Initial QC", "Germline", 'Somatic Tumor-Normal',
'Somatic Tumor-Only'
]
Pipelines = [
"initialqc", "exomeseq-germline", "exomeseq-somatic",
"exomeseq-somatic-tumoronly"
]
self.label2pipeline = {k: v for k, v in zip(PipelineLabels, Pipelines)}
Pipeline = self.Pipeline = StringVar()
PipelineLabel = self.PipelineLabel = StringVar()
self.Pipeline = StringVar()
PipelineLabel.set(PipelineLabels[0])
om = OptionMenu(eframe,
PipelineLabel,
*PipelineLabels,
command=self.option_controller)
#om.config()#bg = widgetBgColor,fg=widgetFgColor)
#om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3, column=1, sticky=W, padx=10, pady=5)
targetsL = Label(eframe, text="Target Capture Kit")
#,fg=textLightColor,bg=baseColor)
targetsL.grid(row=5, column=0, sticky=W, padx=10, pady=5)
targetsE = Entry(eframe, textvariable=self.targetspath, width=50)
label_ref_text = "By default, the path to the Agilent SureSelect V7 targets file is filled in here"
if self.genome == "hg19":
self.targetspath.set(
"/data/CCBR_Pipeliner/db/PipeDB/lib/Agilent_SSv7_allExons_hg19.bed"
)
elif self.genome == "hg38":
self.targetspath.set(
"/data/CCBR_Pipeliner/db/PipeDB/lib/Agilent_SSv7_allExons_hg38.bed"
)
else:
self.targetspath.set(
"/data/CCBR_Pipeliner/db/PipeDB/lib/SureSelect_mm10.bed")
label_ref_text = "By default, the path to the Agilent SureSelect Mouse All Exon V1 targets file is filled in here"
targetsE.grid(row=5, column=1, columnspan=6, sticky=W, padx=10, pady=5)
self.targetspath.trace(
'w', lambda a, b, c, x="targetspath": self.makejson(x))
label = Label(eframe, text=label_ref_text)
label.grid(row=6, column=0, columnspan=5, sticky=W, padx=10, pady=5)
def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self, text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)
label = Label(eframe,
text="Pipeline") #,fg=textLightColor,bg=baseColor)
label.grid(row=3, column=0, sticky=W, padx=10, pady=5)
Pipelines = ["initialqcrnaseq", "rnaseq"]
Pipeline = self.Pipeline = StringVar()
Pipeline.set(Pipelines[0])
om = OptionMenu(eframe,
Pipeline,
*Pipelines,
command=self.option_controller)
om.config() #bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config() #bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3, column=1, sticky=W, padx=10, pady=5)
rReadlens = [
'Read Length is 50', 'Read Length is 75', 'Read Length is 100',
'Read Length is 125', 'Read Length is 150', 'Read Length is 250'
]
self.rReadlen = rReadlen = StringVar()
rReadlen.set(rReadlens[2])
self.om2 = OptionMenu(eframe,
rReadlen,
*rReadlens,
command=self.option_controller)
#self.om2.grid(row=4,column=1,sticky=W,padx=10,pady=5)
rStrands = [
'0, Reads are Unstranded', '1, Reads are from Sense Strand',
'2, Reads are from Anti-Sense Strand'
]
self.rStrand = rStrand = StringVar()
rStrand.set(rStrands[0])
self.om3 = OptionMenu(eframe,
rStrand,
*rStrands,
command=self.option_controller)
#self.om3.grid(row=5,column=1,sticky=W,padx=10,pady=5)
rDegs = [
"no, Do not Report Differentially Expressed Genes",
"yes, Report Differentially Expressed Genes"
]
self.rDeg = rDeg = StringVar()
rDeg.set(rDegs[0])
self.om4 = OptionMenu(eframe,
rDeg,
*rDegs,
command=self.option_controller)
self.om4.grid(row=6, column=1, sticky=W, padx=10, pady=5)
#####################
#Sample Threshold
#####################
self.sampleLF = sampleLF = LabelFrame(
eframe, text="Low Abundance Gene Thresholds")
self.rMincount = rMincount = StringVar()
rMincount.set("5")
self.rMinsamples = rMinsamples = StringVar()
rMinsamples.set("2")
#rMincount.trace('w', lambda a,b,c,x="rmincount": makejson(x))
#Filter out genes < [5] read counts in < [2] samples
rminsamplesL = Label(sampleLF, text="Include genes with >=") # in")
rmincountE = Entry(sampleLF, bd=2, width=3, textvariable=rMincount)
rmincountL = Label(sampleLF, text="read counts in >=")
rminsamplesE = Entry(sampleLF, bd=2, width=3, textvariable=rMinsamples)
rminsamplesR = Label(sampleLF, text="samples")
rminsamplesL.grid(row=9, column=1, sticky=W, padx=10, pady=5)
rmincountE.grid(row=9, column=2, sticky=W, padx=0, pady=5)
rmincountL.grid(row=9, column=3, sticky=W, padx=5, pady=5)
rminsamplesE.grid(row=9, column=4, sticky=W, padx=0, pady=5)
rminsamplesR.grid(row=9, column=5, sticky=W, padx=10, pady=5)
#rMinsamples.trace('w', lambda a,b,c,x="rmincount": makejson(x))
sampleLF.grid(row=8,
column=0,
columnspan=4,
sticky=W,
padx=20,
pady=10)
#####################
self.add_info(eframe)
self.option_controller()
def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self,text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
label = Label(eframe,text="Pipeline")#,fg=textLightColor,bg=baseColor)
label.grid(row=3,column=0,sticky=W,padx=10,pady=5)
PipelineLabels=["CellRanger","Initial/QC","Clustering","Multi-Sample Clustering" ]
Pipelines=["cellranger","scrnaseqinit","scrnaseqcluster", "scrnaseqmulticluster"]
self.label2pipeline = { k:v for k,v in zip(PipelineLabels, Pipelines)}
PipelineLabel = self.PipelineLabel = StringVar()
self.Pipeline = StringVar()
PipelineLabel.set(PipelineLabels[0])
om = OptionMenu(eframe, PipelineLabel, *PipelineLabels, command=self.option_controller)
om.config()#bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3,column=1,sticky=W,padx=10,pady=5)
self.crOpts = crOpts = LabelFrame( eframe,
text="CellRanger Settings" )
self.scrCRID = scrCRID = StringVar()
scrCRID.set("SPECIFY_PREFIX_HERE")
self.scrExpected = scrExpected = StringVar()
scrExpected.set("3000")
scrcridL = Label(crOpts, text="CellRanger Sample ID: ")
scrcridE = Entry(crOpts, bd =2, width=25, textvariable=scrCRID)
scrcridL.grid(row=9,column=1,sticky=W,padx=10,pady=5)
scrcridE.grid(row=9,column=2,sticky=W,padx=0,pady=5)
screxpectedL = Label(crOpts, text="Expected number of cells: ")
screxpectedE = Entry(crOpts, bd =2, width=8, textvariable=scrExpected)
screxpectedL.grid(row=10,column=1,sticky=W,padx=10,pady=5)
screxpectedE.grid(row=10,column=2,sticky=W,padx=0,pady=5)
self.clusterOpts = clusterOpts = LabelFrame( eframe,
text="Clustering and tSNE Options" )
self.scrPCs = scrPCs = StringVar()
scrPCs.set("12")
self.scrRes = scrRes = StringVar()
scrRes.set("0.6")
#scrPCs.trace('w', lambda a,b,c,x="scrPCs": makejson(x))
#Filter out genes < [5] read counts in < [2] samples
scrpcsL = Label(clusterOpts, text="Include principal components 1 through ")
scrpcsE = Entry(clusterOpts, bd =2, width=3, textvariable=scrPCs)
scrresL = Label(clusterOpts, text="with clustering resolution: ")
scrresE = Entry(clusterOpts, bd =2, width=3, textvariable=scrRes)
scrpcsL.grid(row=9,column=1,sticky=W,padx=10,pady=5)
scrpcsE.grid(row=9,column=2,sticky=W,padx=0,pady=5)
scrresL.grid(row=9,column=3,sticky=W,padx=5,pady=5)
scrresE.grid(row=9,column=4,sticky=W,padx=0,pady=5)
#scrRes.trace('w', lambda a,b,c,x="scrPCs": makejson(x))
clusterOpts.grid( row=8, column=0, columnspan=4, sticky=W, padx=20, pady=10 )
self.multiclusterOpts = multiclusterOpts = LabelFrame( eframe,
text = "Multi-Sample Clustering and tSNE Options")
scrccsL = Label(multiclusterOpts, text="Include canonical components 1 through ")
scrccsE = Entry(multiclusterOpts, bd =2, width=3, textvariable=scrPCs)
scrmcresL = Label(multiclusterOpts, text="with clustering resolution: ")
scrmcresE = Entry(multiclusterOpts, bd =2, width=3, textvariable=scrRes)
scrccsL.grid(row=9,column=1,sticky=W,padx=10,pady=5)
scrccsE.grid(row=9,column=2,sticky=W,padx=0,pady=5)
scrmcresL.grid(row=9,column=3,sticky=W,padx=5,pady=5)
scrmcresE.grid(row=9,column=4,sticky=W,padx=0,pady=5)
self.qcOpts = qcOpts = LabelFrame( eframe,
text="Initial Settings" )
countL = Label( qcOpts, text="Counts/Matrix Dir:" )
countL.grid(row=9, column=1, sticky=W, padx=10, pady=5 )
countpath=StringVar()
self.countpath = countpath
count_entry = Entry(qcOpts,
bd =2,
width = 50,
#bg = entryBgColor,
#fg = entryFgColor,
textvariable = countpath, state='normal'
)
count_entry.grid( row=9, column=2, columnspan=3 )
self.count_button = count_button = Button( qcOpts,
text="Open Directory",
command=self.set_count_directory )
count_button.grid( row=9, column=5 )
self.mattype = mattype = StringVar()
mattypeL = Label(qcOpts, text="Count matrix format: ")
scrMatTypeDropdown = ["cellranger", "cellranger_raw", "zumi", "biorad"]
mattype.set(scrMatTypeDropdown[0])
mattype_om = OptionMenu(qcOpts, mattype, *scrMatTypeDropdown)
mattypeL.grid(row=10,column=1,sticky=W,padx=10,pady=5)
mattype_om.grid(row=10,column=2,sticky=W,padx=0,pady=5)
self.docycleregress = docycleregress = StringVar()
docycleregressL = Label(qcOpts, text="Do cell cycle regression? ")
scrCycleDropdown = ["TRUE", "FALSE"]
docycleregress.set(scrCycleDropdown[0])
cycle_om = OptionMenu(qcOpts, docycleregress, *scrCycleDropdown)
docycleregressL.grid(row=11,column=1,sticky=W,padx=10,pady=5)
cycle_om.grid(row=11,column=2,sticky=W,padx=0,pady=5)
usecycleregressL_c = Label(clusterOpts, text="Use cell cycle regressed data? ")
docycleregress.set(scrCycleDropdown[0])
cycle_om_c = OptionMenu(clusterOpts, docycleregress, *scrCycleDropdown)
usecycleregressL_c.grid(row=10,column=1,sticky=W,padx=10,pady=5)
cycle_om_c.grid(row=10,column=2,sticky=W,padx=0,pady=5)
usecycleregressL_mc = Label(multiclusterOpts, text="Use cell cycle regressed data? ")
docycleregress.set(scrCycleDropdown[0])
cycle_om_mc = OptionMenu(multiclusterOpts, docycleregress, *scrCycleDropdown)
usecycleregressL_mc.grid(row=10,column=1,sticky=W,padx=10,pady=5)
cycle_om_mc.grid(row=10,column=2,sticky=W,padx=0,pady=5)
groups_buttonL = Label(qcOpts, text="SAMPLE INFORMATION: ")
groups_button = Button(qcOpts,
text="Set Groups",
command = self.popup_groups )
groups_buttonL.grid(row=12,column=1,sticky=W,padx=10,pady=5)
groups_button.grid(row=12,column=2,sticky=W,padx=0,pady=5)
#####################
self.option_controller()
def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self, text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)
label = Label(eframe,
text="Pipeline") #,fg=textLightColor,bg=baseColor)
label.grid(row=3, column=0, sticky=W, padx=10, pady=5)
PipelineLabels = ["Initial QC", "Differential Expression"]
Pipelines = ["scrnaQC", "scrnaDE"]
self.label2pipeline = {k: v for k, v in zip(PipelineLabels, Pipelines)}
PipelineLabel = self.PipelineLabel = StringVar()
self.Pipeline = StringVar()
PipelineLabel.set(PipelineLabels[0])
om = OptionMenu(eframe,
PipelineLabel,
*PipelineLabels,
command=self.option_controller)
om.config() #bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config() #bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3, column=1, sticky=W, padx=10, pady=5)
######## QUALITY CONTROL/FILTERING/CLUSTERING ###############
self.qcOptions = qcOptions = LabelFrame(
eframe, text="QC, Filtering, and Initial Clustering")
#algorithm selection
self.clustAlg = clustAlg = StringVar()
clustAlgLabel = Label(qcOptions, text="Clustering Algorithm: ")
clustAlgDropdown = [
"SLM (Smart Local Moving)", "Louvain (Original)",
"Louvain (with Multilevel Refinement)"
]
clustAlg.set(clustAlgDropdown[0])
clustAlgOptMenu = OptionMenu(qcOptions, clustAlg, *clustAlgDropdown)
clustAlgLabel.grid(row=8, column=1, sticky=W, padx=10, pady=5)
clustAlgOptMenu.grid(row=8, column=2, sticky=W, padx=0, pady=5)
#clustering resolutions
self.resolution = resolution = StringVar()
resolution.set("0.4,0.6,0.8,1.0,1.2")
resolutionLabel = Label(
qcOptions, text="Clustering Resolution(s): \nSeparate with commas")
resolutionEntry = Entry(qcOptions,
bd=2,
width=25,
textvariable=resolution)
resolutionLabel.grid(row=9, column=1, sticky=W, padx=10, pady=5)
resolutionEntry.grid(row=9, column=2, sticky=W, padx=0, pady=5)
#annotation db: human: HPCA/BP Encode; mouse: immgen/mouseRNAseq
self.annotDB = annotDB = StringVar()
annotLabel = Label(qcOptions, text="Annotation database: ")
annotHuman = ["HPCA", "BP Encode"]
annotMouse = ["immgen", "mouseRNAseq"]
annotDropdown = []
genome = self.global_info.annotation.get()
if (genome == "GRCh38"):
annotDropdown = annotHuman.copy()
elif (genome == "mm10"):
annotDropdown = annotMouse.copy()
else:
annotDropdown.append("No genome selected")
annotDB.set(annotDropdown[0])
annotDB_om = OptionMenu(qcOptions, annotDB, *annotDropdown)
annotLabel.grid(row=10, column=1, sticky=W, padx=10, pady=5)
annotDB_om.grid(row=10, column=2, sticky=W, padx=0, pady=5)
#set groups, mostly for relabeling purposes
self.add_info(qcOptions) #Position 11
# self.option_controller()
# groups_buttonL = Label(qcOptions, text="Sample Information: ")
# groups_button = Button(qcOptions,
# text="Set Groups",
# command = self.popup_groups )
# groups_buttonL.grid(row=12,column=1,sticky=W,padx=10,pady=5)
# groups_button.grid(row=12,column=2,sticky=W,padx=0,pady=5)
#
#
######### DIFFERENTIAL EXPRESSION #########
self.deOptions = deOptions = LabelFrame(
eframe, text="Differential Gene Expression")
#option for cluster resolution for DE
self.resolutionDE = resolutionDE = StringVar()
resolutionDE.set("0.8")
resolutionDELabel = Label(
deOptions,
text=
"Clustering Resolution: \nChoose a previous resolution or \nselect a new resolution to run"
)
resolutionDEEntry = Entry(deOptions,
bd=2,
width=25,
textvariable=resolutionDE)
resolutionDELabel.grid(row=10, column=1, sticky=W, padx=10, pady=5)
resolutionDEEntry.grid(row=10, column=2, sticky=W, padx=0, pady=5)
#option for merged/integrated object
# self.integrateOption = integrateOption = StringVar()
# integrateLabel = Label(deOptions, text="Merged or Integrated (batch corrected): ")
# integrateDropdown = ["Merged","Integrated"]
# integrateOption.set(integrateDropdown[0])
# integrateOptMenu = OptionMenu(deOptions, integrateOption, *integrateDropdown)
# integrateLabel.grid(row=9,column=1,sticky=W,padx=10,pady=5)
# integrateOptMenu.grid(row=9,column=2,sticky=W,padx=0,pady=5)
self.add_info(deOptions) #Position 11
self.option_controller()
