def _plot_with_rpy2(self, regions, filename):
from rpy2 import robjects
import rpy2.robjects.lib.ggplot2 as ggplot2
from rpy2.robjects.lib import grid
from rpy2.robjects.packages import importr
grdevices = importr('grDevices')
base = importr('base')
grdevices.pdf(file=filename + '.pdf')
t = [x for x in range(-self.num_bins, self.num_bins + 1)]
for region in regions[:self.num_regs]:
if not np.any(region.weighted):
logger.warning(
"Warning: No data for region located on bin " + str(region.bin) + ". Not plotting this one.")
continue
middle = (len(region.weighted[0]) - 1) / 2
if middle < self.num_bins:
logger.error("Warning: There are less bins calculated for regions than you want to plot.")
sys.exit(1)
d = {'map': robjects.StrVector(
[str(m) for sublist in [[x] * len(t) for x in range(len(region.weighted))] for m in sublist]),
't': robjects.FloatVector(t * len(region.weighted)),
'e': robjects.FloatVector([i for sublist in region.weighted for i in
sublist[middle - self.num_bins:middle + self.num_bins + 1]]),
'p': robjects.FloatVector([-np.log10(x) for sublist in region.pvalues for x in
sublist[middle - self.num_bins:middle + self.num_bins + 1]]),
'c': robjects.FloatVector([-np.log10(x) for sublist in region.corrected_pvalues for x in
sublist[middle - self.num_bins:middle + self.num_bins + 1]])}
dataf = robjects.DataFrame(d)
gp = ggplot2.ggplot(dataf) # first yellow second red
p1 = gp + ggplot2.geom_line(mapping=ggplot2.aes_string(x='t', y='e', group='map', colour='map'),
alpha=0.8) + ggplot2.scale_y_continuous(trans='log2') + ggplot2.ggtitle(
"\n".join(wrap("Bin " + str(region.bin) + " : " + str(region.positions)))) + ggplot2.labs(
y="log Intensity") + ggplot2.theme_classic() + ggplot2.theme(
**{'axis.title.x': ggplot2.element_blank(), 'axis.text.y': ggplot2.element_text(angle=45),
'axis.text.x': ggplot2.element_blank(),
'legend.position': 'none'}) + ggplot2.scale_colour_brewer(palette="Set1")
p2 = gp + ggplot2.geom_line(mapping=ggplot2.aes_string(x='t', y='p', group='map', colour='map'),
alpha=0.8) + ggplot2.labs(
y="-log10(p-value)") + ggplot2.theme_classic() + ggplot2.theme(
**{'axis.title.x': ggplot2.element_blank(), 'axis.text.x': ggplot2.element_blank(),
'legend.position': 'none'}) + ggplot2.scale_colour_brewer(palette="Set1")
p3 = gp + ggplot2.geom_line(mapping=ggplot2.aes_string(x='t', y='c', group='map', colour='map'),
alpha=0.8) + ggplot2.labs(y="-log10(q-value)",
x='bins (' + str(self.bin_res) + ' bp each)') + \
ggplot2.geom_hline(mapping=ggplot2.aes_string(yintercept=str(-np.log10(self.threshold))),
colour='black', alpha=0.8, linetype='dashed') + ggplot2.theme_classic() + \
ggplot2.theme(**{'legend.position': 'none'}) + ggplot2.scale_colour_brewer(palette="Set1")
g1 = ggplot2.ggplot2.ggplotGrob(p1)
g2 = ggplot2.ggplot2.ggplotGrob(p2)
g3 = ggplot2.ggplot2.ggplotGrob(p3)
robjects.globalenv["g"] = base.rbind(g1, g2, g3, size='first')
robjects.r("grid::grid.draw(g)")
grid.newpage()
logger.debug('Plotted region ' + str(region.bin))
grdevices.dev_off()
def makeImage(rates):
out = tempfile.NamedTemporaryFile(suffix='.png')
grdevices = importr('grDevices')
grdevices.png(file=out.name, width=512, height=512)
try:
grid.newpage()
lt = grid.layout(1, 1)
vp = grid.viewport(layout=lt)
vp.push()
vp = grid.viewport(**{'layout.pos.col': 1, 'layout.pos.row': 1})
for row, (year, count) in enumerate(sorted(rates['byYear'].items())):
grid.rect(x=grid.unit(.5, "npc"),
y=grid.unit(row / len(rates['byYear']), "npc"),
width=grid.unit(count / 15000, "npc"),
height=grid.unit(.95 / len(rates['byYear']), "npc"),
vp=vp).draw()
finally:
grdevices.dev_off()
return open(out.name).read()
def makeImage(rates):
out = tempfile.NamedTemporaryFile(suffix='.png')
grdevices = importr('grDevices')
grdevices.png(file=out.name, width=512, height=512)
try:
grid.newpage()
lt = grid.layout(1, 1)
vp = grid.viewport(layout = lt)
vp.push()
vp = grid.viewport(**{'layout.pos.col':1, 'layout.pos.row': 1})
for row, (year, count) in enumerate(sorted(rates['byYear'].items())):
grid.rect(x=grid.unit(.5, "npc"),
y=grid.unit(row / len(rates['byYear']), "npc"),
width=grid.unit(count / 15000, "npc"),
height=grid.unit(.95 / len(rates['byYear']), "npc"),
vp = vp).draw()
finally:
grdevices.dev_off()
return open(out.name).read()
gp = ggplot2.ggplot(mtcars)
pp = gp + \
ggplot2.aes_string(x='wt', y='mpg') + \
ggplot2.geom_point()
pp.plot()
#-- ggplot2mtcars-end
grdevices.dev_off()
grdevices.png('../../_static/graphics_ggplot2geombin2d.png',
width=1000,
height=350,
antialias="subpixel",
type="cairo")
grid.newpage()
grid.viewport(layout=grid.layout(1, 3)).push()
vp = grid.viewport(**{'layout.pos.col': 1, 'layout.pos.row': 1})
#-- ggplot2geombin2d-begin
gp = ggplot2.ggplot(dataf_rnorm)
pp = gp + \
ggplot2.aes_string(x='value', y='other_value') + \
ggplot2.geom_bin2d() + \
ggplot2.ggtitle('geom_bin2d')
pp.plot(vp=vp)
#-- ggplot2geombin2d-end
vp = grid.viewport(**{'layout.pos.col': 2, 'layout.pos.row': 1})
#-- ggplot2geomdensity2d-begin
grdevices.png('../../_static/graphics_ggplot2mtcars.png',
width = 612, height = 612, antialias="subpixel", type="cairo")
#-- ggplot2mtcars-begin
gp = ggplot2.ggplot(mtcars)
pp = gp + \
ggplot2.aes_string(x='wt', y='mpg') + \
ggplot2.geom_point()
pp.plot()
#-- ggplot2mtcars-end
grdevices.dev_off()
grdevices.png('../../_static/graphics_ggplot2geombin2d.png',
width = 1000, height = 350, antialias="subpixel", type="cairo")
grid.newpage()
grid.viewport(layout=grid.layout(1, 3)).push()
vp = grid.viewport(**{'layout.pos.col':1, 'layout.pos.row': 1})
#-- ggplot2geombin2d-begin
gp = ggplot2.ggplot(dataf_rnorm)
pp = gp + \
ggplot2.aes_string(x='value', y='other_value') + \
ggplot2.geom_bin2d() + \
ggplot2.opts(title = 'geom_bin2d')
pp.plot(vp = vp)
#-- ggplot2geombin2d-end
vp = grid.viewport(**{'layout.pos.col':2, 'layout.pos.row': 1})
#-- ggplot2geomdensity2d-begin
