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dm = dm.drop('extra', axis=1)
# -------------------------------------------------------------------------
#
# Preparing diagram
#
# -------------------------------------------------------------------------
message("Preparing diagram")
p = ggplot(data=dm, mapping=aes('pos',
'gene')) + geom_tile(aes(fill='exprs'))
p += theme_bw()
p += theme(legend_text=element_text(size=6),
panel_grid_major=element_blank(),
panel_grid_minor=element_blank(),
panel_border=element_rect(colour="black", size=1),
legend_key_size=2,
legend_position="top",
legend_key=element_rect(colour="white"),
axis_text_y=element_text(colour="#333333",
size=4),
axis_line=element_line(size=0.1, colour=""),
axis_text_x=element_text(colour="#333333",
size=6, angle=65,
face="plain"),
axis_title_x=element_text(colour="#333333",
size=8, angle=0,
face="plain"),
axis_title_y=element_text(colour="#333333",
size=8, angle=90,
if display_fit_quality:
fit_qual_text = dm[statname + '_negbinom_fit_quality'].append(na_series)
fit_qual_text.index = range(len(fit_qual_text))
text_with_fit = list()
for t, f in zip(text.tolist(), fit_qual_text.tolist()):
text_with_fit += [t + "\n" + 'fit={0:.2g}'.format(f)]
text = pd.Series(text_with_fit)
aes_plot = aes(x='Feature', y=text_pos, label=text)
p += geom_label(mapping=aes_plot, stat='identity',
size=5, boxstyle='round', label_size=0.2,
color='white', fill=signif_color)
# Theme
p += theme(legend_title=element_blank(),
legend_position="top",
legend_box_spacing=0.65,
legend_key_size=8,
legend_text=element_text(size=8),
legend_key=element_blank(),
axis_title_x=element_blank(),
axis_title_y=element_text(colour='#333333',
size=8,
hjust=4,
angle=90,
face="plain"),
axis_text_y=element_text(size=5,
margin={'r': 0},
angle=0),
axis_text_x=element_text(size=5,
angle=45)
elif grid_axis == 'x':
drop_grid.update(['panel_grid_major_y', 'panel_grid_minor_y'])
if grid_lines == 'major':
drop_grid.add('panel_grid_minor_y')
elif grid_lines == 'minor':
drop_grid.add('panel_grid_major_y')
elif grid_axis == 'y':
drop_grid.update(['panel_grid_major_x', 'panel_grid_minor_x'])
if grid_lines == 'major':
drop_grid.add('panel_grid_minor_x')
elif grid_lines == 'minor':
drop_grid.add('panel_grid_major_x')
grid_opt = dict()
for x in drop_grid:
grid_opt[x] = gg.element_blank()
return getattr(gg, 'theme_'+theme)() + \
gg.theme(panel_border = gg.element_blank(),
axis_line = gg.element_line(color = "black"),
**grid_opt)
def hide_axis_ticks_x(self):
return self._change_theme('axis_ticks_major_x', p9.element_blank())
size=7,
angle=rotate_x_label),
strip_background=element_rect(colour="#000000",
fill="#000000")
)
p += scale_fill_gradientn(colors=color_palette_list,
name="Signal", na_value="#222222")
p += plotnine.labels.xlab(xlabel)
p += plotnine.labels.ylab("Genes")
if not show_row_names:
p += theme(axis_text_y=element_blank(),
axis_ticks_major_y=element_blank(),
axis_ticks_minor_y=element_blank())
if config['ft_type'] in ["transcript", "user_regions"]:
if config['from']:
if config['to']:
ticks = [0, bin_nb_ups / 2] + list(np.linspace(bin_nb_ups, bin_nb_main + bin_nb_ups, 11)) + [
bin_nb_total - bin_nb_dws / 2, bin_nb_total]
ticks = [x / bin_nb_total * 100 for x in ticks]
labels = [-fr,
round(-fr / 2, 0)
] + [str(x) + "%" for x in np.linspace(0, 100, 11)] + [round(to / 2, 0), to]
else:
ticks = [0, bin_nb_ups / 2] + list(np.linspace(bin_nb_ups, bin_nb_total, 11))
for t, f in zip(text.tolist(), fit_qual_text.tolist()):
text_with_fit += [t + "\n" + 'fit={0:.2g}'.format(f)]
text = pd.Series(text_with_fit)
aes_plot = aes(x='Feature', y=text_pos, label=text)
p += geom_label(mapping=aes_plot, stat='identity',
size=5, boxstyle='round', label_size=0.2,
color='white', fill=signif_color)
# Theme
p += theme(legend_title=element_blank(),
legend_position="top",
legend_box_spacing=0.65,
legend_key_size=8,
legend_text=element_text(size=8),
legend_key=element_blank(),
axis_title_x=element_blank(),
axis_title_y=element_text(colour='#333333',
size=8,
hjust=4,
angle=90,
face="plain"),
axis_text_y=element_text(size=5,
margin={'r': 0},
angle=0),
axis_text_x=element_text(size=5,
angle=45)
)
# Add a nicer set of colors.
p += scale_fill_manual(values={'Shuffled': '#757575', 'True': '#0288d1'})
def hide_axis_ticks_y(self):
return self._change_theme('axis_ticks_major_y', p9.element_blank())
# -------------------------------------------------------------------------
#
# Preparing diagram
#
# -------------------------------------------------------------------------
message("Preparing diagram")
p = ggplot(data=dm, mapping=aes('pos',
'gene')) + geom_tile(aes(fill='exprs'))
p += theme_bw()
p += theme(legend_text=element_text(size=6),
panel_grid_major=element_blank(),
panel_grid_minor=element_blank(),
panel_border=element_rect(colour="black", size=1),
legend_key_size=2,
legend_position="top",
legend_key=element_rect(colour="white"),
axis_text_y=element_text(colour="#333333",
size=4),
axis_line=element_line(size=0.1, colour=""),
axis_text_x=element_text(colour="#333333",
size=6, angle=65,
face="plain"),
axis_title_x=element_text(colour="#333333",
size=8, angle=0,
face="plain"),
axis_title_y=element_text(colour="#333333",
size=8, angle=90,
face="plain"),