cr.selection_glyph = Circle(fill_color=cls_color_mapper,
line_color=cls_color_mapper)
cr.nonselection_glyph = Circle(fill_color=cls_color_mapper,
line_color=cls_color_mapper,
fill_alpha=0.05,
line_alpha=0.05)
color_bar = ColorBar(color_mapper=LinearColorMapper(palette="Viridis256",
low=1,
high=10),
label_standoff=12,
border_line_color=None,
location=(0, 0))
p.add_layout(color_bar, 'right')
color_bar.visible = False
if type(cls_color_mapper['transform']) is LinearColorMapper:
color_bar.color_mapper = cls_color_mapper['transform']
# p.add_layout(color_bar, 'right')
color_bar.visible = True
# Define widgets
hover_tip_tool = HoverTool(tooltips=generate_tooltip_html(),
show_arrow=False,
renderers=[cr])
wheel_zoom_tool = WheelZoomTool()
file_select_dropdown = Dropdown(label="Data file",
button_type="warning",
height_policy='min',
menu=[('refresh list', 'refresh_list'), None])
update_file_list()
color_class_select = Select(title="Colored by:",
value=features_list[0],
options=features_list[:],
def GENE(self):
def gcw(*args, **kwargs):
return self.ccwidget('geneview_' + args[0],
*args[1:],
**kwargs,
setnamer='gene')
#widgets
w = dict(
gene=gcw('gene_name', 'text'),
warn=widgets.HTML(),
)
# data
samples = self.counttable.columns
nosamples = len(samples)
#gene mapper
gmapper = CMAPPER(self, name='gene')
gmapper.method = 'gene'
defgene = self.counttable.std(1).sort_values().tail(1).index[0]
gmapper.value = defgene
w['gene'].value = defgene
#color mapper
cmapper = CMAPPER(self, name='color')
cmapper.method = 'metadata'
cmapper.value = 'plate'
#sort order
smapper = CMAPPER(self, name='sort')
smapper2 = CMAPPER(self, name='sort 2')
def get_sort_order():
sdf = pd.DataFrame({
1: smapper.score.sort_values(),
2: smapper2.score.sort_values()
})
sdf = sdf.sort_values(by=[1, 2])
return sdf.index
sort_order = get_sort_order()
pdata = ColumnDataSource(
dict(
x=pd.Series(range(nosamples), index=sort_order),
y=gmapper.score.loc[sort_order],
score=cmapper.score.loc[sort_order],
))
pdata2 = pd.DataFrame(
dict(
x=pd.Series(range(nosamples), index=sort_order),
y=gmapper.score.loc[sort_order],
score=cmapper.score.loc[sort_order],
))
bfigure = bokeh_figure(
plot_width=FIGSIZE[0],
plot_height=int(FIGSIZE[1] * 0.8),
# tools = bokeh_tools,
y_range=bmodels.Range1d(gmapper.min(), gmapper.max()),
toolbar_sticky=False,
toolbar_location='left',
title='geneplot')
#bbar = bokeh_chart.Bar(pdata2, 'x', values='y', group='plate')
bfigure.title.text_color = 'darkgrey'
bfigure.title.text_font_style = 'normal'
bfigure.title.text_font_size = "12px"
bplot = bfigure.vbar(x='x',
width=0.5,
bottom=0,
top='y',
source=pdata,
legend='score',
color=dict(field='score',
transform=cmapper.colormapper))
blegend = bfigure.legend[0].items[0]
bcolorbar = ColorBar(color_mapper=gmapper.colormapper,
ticker=BasicTicker(),
formatter=BasicTickFormatter(precision=1),
label_standoff=10,
border_line_color=None,
location=(0, 0))
null_colorbar_mapper = LinearColorMapper(palette='Inferno256',
low=0,
high=0)
if cmapper.discrete:
#remove ColorBar
bcolorbar.color_mapper = null_colorbar_mapper
else:
#remove legend
bfigure.legend[0].items.pop(
) #remove legend - we can add this later again
bfigure.add_layout(bcolorbar, 'right')
# # display widgets
display(ilabel('gene', w['gene']))
cmapper.display()
smapper.display()
smapper2.display()
display(w['warn'])
#for k, v in bplot.data_source.data.items():
# print(k, v.shape, v.dropna().shape)
bhandle = bokeh_io.show(bfigure, notebook_handle=True)
#bhandle = bokeh_io.show(bbar, notebook_handle=True)
def warn(message):
w['warn'].value = '<b>{}</b>'.format(message)
def on_gene_change(*args):
gene = w['gene'].value
if not gene in self.counttable.index:
warn("gene {} is not in current counttable".format(gene))
return
sortorder = get_sort_order()
gmapper.value = gene
yval = gmapper.score.loc[sortorder]
bplot.data_source.data['y'] = yval
bokeh_io.push_notebook(handle=bhandle)
def on_sort_change(*args):
order = get_sort_order()
d = bplot.data_source.data
d['x'].index = order
d['y'] = d['y'].loc[order]
d['score'] = d['score'].loc[order]
bokeh_io.push_notebook(handle=bhandle)
def on_color_change(*args):
order = get_sort_order()
score = cmapper.score
score = score.loc[order]
bplot.data_source.data['score'] = score
bplot.glyph.fill_color['transform'] = cmapper.colormapper
cm = cmapper.colormapper
self._cm = cm
if cmapper.discrete:
warn('discrete')
bcolorbar.color_mapper = null_colorbar_mapper
if not bfigure.legend[0].items:
bfigure.legend[0].items.append(blegend)
else:
warn('cont')
bcolorbar.color_mapper = cmapper.colormapper
if bfigure.legend[0].items:
bfigure.legend[0].items.pop()
bokeh_io.push_notebook(handle=bhandle)
smapper.on_change = on_sort_change
smapper2.on_change = on_sort_change
cmapper.on_change = on_color_change
w['gene'].on_submit(on_gene_change)
on_gene_change
on_color_change
on_sort_change
