def line_plot(pdf_file,
data,
x,
y,
var,
null_label="N/A",
linetype=None,
title=None,
xlab=None,
ylab=None,
colorname=None,
linename=None,
**extra_aes_params):
pdf(pdf_file, width=11.7, height=8.3, paper="a4r")
if any(data[x].isnull()):
labels = [null_label] + map(str, sorted(set(
data[data[x].notnull()][x])))
labels = robjects.StrVector(labels)
nulls = data[x].isnull()
label_vals = dict(zip(labels, range(len(labels))))
data[x] = data[x].astype("str")
data[x][nulls] = null_label
data['sortcol'] = data[x].map(label_vals.__getitem__)
data.sort('sortcol', inplace=True)
else:
labels = None
if linetype and linetype != var:
data['group'] = data[var].map(str) + data[linetype].map(str)
else:
data['group'] = data[var]
rdata = common.convert_to_r_dataframe(data)
if labels:
ix = rdata.names.index(x)
rdata[ix] = ordered(rdata[ix], levels=labels)
gp = gg2.ggplot(rdata)
pp = (
gp + gg2.geom_point(size=3) +
gg2.scale_colour_hue(name=(colorname or var)) +
#gg2.scale_colour_continuous(low="black") +
gg2.aes_string(x=x, y=y, color=var, variable=var) +
ggtitle(title or "") + xlabel(xlab or x) + ylabel(ylab or y) #+
#gg2.scale_y_continuous(breaks=seq(0.0, 1.0, 0.05))
)
# line type stuff
if linetype:
pp += gg2.geom_path(gg2.aes_string(group='group', linetype=linetype),
size=0.5)
pp += gg2.scale_linetype(name=(linename or linetype))
else:
pp += gg2.geom_path(gg2.aes_string(group='group'), size=0.5)
pp.plot()
dev_off()
def line_plot(
pdf_file,
data,
x,
y,
var,
null_label="N/A",
linetype=None,
title=None,
xlab=None,
ylab=None,
colorname=None,
linename=None,
**extra_aes_params
):
pdf(pdf_file, width=11.7, height=8.3, paper="a4r")
if any(data[x].isnull()):
labels = [null_label] + map(str, sorted(set(data[data[x].notnull()][x])))
labels = robjects.StrVector(labels)
nulls = data[x].isnull()
label_vals = dict(zip(labels, range(len(labels))))
data[x] = data[x].astype("str")
data[x][nulls] = null_label
data["sortcol"] = data[x].map(label_vals.__getitem__)
data.sort("sortcol", inplace=True)
else:
labels = None
if linetype and linetype != var:
data["group"] = data[var].map(str) + data[linetype].map(str)
else:
data["group"] = data[var]
rdata = common.convert_to_r_dataframe(data)
if labels:
ix = rdata.names.index(x)
rdata[ix] = ordered(rdata[ix], levels=labels)
gp = gg2.ggplot(rdata)
pp = (
gp
+ gg2.geom_point(size=3)
+ gg2.scale_colour_hue(name=(colorname or var))
+
# gg2.scale_colour_continuous(low="black") +
gg2.aes_string(x=x, y=y, color=var, variable=var)
+ ggtitle(title or "")
+ xlabel(xlab or x)
+ ylabel(ylab or y) # +
# gg2.scale_y_continuous(breaks=seq(0.0, 1.0, 0.05))
)
# line type stuff
if linetype:
pp += gg2.geom_path(gg2.aes_string(group="group", linetype=linetype), size=0.5)
pp += gg2.scale_linetype(name=(linename or linetype))
else:
pp += gg2.geom_path(gg2.aes_string(group="group"), size=0.5)
pp.plot()
dev_off()
def plot(self,
fn,
x='x',
y='y',
col=None,
group=None,
w=1100,
h=800,
size=2,
smooth=True,
point=True,
jitter=False,
boxplot=False,
boxplot2=False,
title=False,
flip=False,
se=False,
density=False,
line=False):
df = self.df
#import math, datetime
grdevices = importr('grDevices')
if not title:
title = fn.split("/")[-1]
grdevices.png(file=fn, width=w, height=h)
gp = ggplot2.ggplot(df)
pp = gp
if col and group:
pp += ggplot2.aes_string(x=x, y=y, col=col, group=group)
elif col:
pp += ggplot2.aes_string(x=x, y=y, col=col)
elif group:
pp += ggplot2.aes_string(x=x, y=y, group=group)
else:
pp += ggplot2.aes_string(x=x, y=y)
if boxplot:
if col:
pp += ggplot2.geom_boxplot(ggplot2.aes_string(fill=col),
color='blue')
else:
pp += ggplot2.geom_boxplot(color='blue')
if point:
if jitter:
if col:
pp += ggplot2.geom_point(ggplot2.aes_string(fill=col,
col=col),
size=size,
position='jitter')
else:
pp += ggplot2.geom_point(size=size, position='jitter')
else:
if col:
pp += ggplot2.geom_point(ggplot2.aes_string(fill=col,
col=col),
size=size)
else:
pp += ggplot2.geom_point(size=size)
if boxplot2:
if col:
pp += ggplot2.geom_boxplot(ggplot2.aes_string(fill=col),
color='blue',
outlier_colour="NA")
else:
pp += ggplot2.geom_boxplot(color='blue')
if smooth:
if smooth == 'lm':
if col:
pp += ggplot2.stat_smooth(ggplot2.aes_string(col=col),
size=1,
method='lm',
se=se)
else:
pp += ggplot2.stat_smooth(col='blue',
size=1,
method='lm',
se=se)
else:
if col:
pp += ggplot2.stat_smooth(ggplot2.aes_string(col=col),
size=1,
se=se)
else:
pp += ggplot2.stat_smooth(col='blue', size=1, se=se)
if density:
pp += ggplot2.geom_density(ggplot2.aes_string(x=x, y='..count..'))
if line:
pp += ggplot2.geom_line(position='jitter')
pp += ggplot2.opts(
**{
'title': title,
'axis.text.x': ggplot2.theme_text(size=24),
'axis.text.y': ggplot2.theme_text(size=24, hjust=1)
})
#pp+=ggplot2.scale_colour_brewer(palette="Set1")
pp += ggplot2.scale_colour_hue()
if flip:
pp += ggplot2.coord_flip()
pp.plot()
grdevices.dev_off()
print ">> saved: " + fn
def plot(self, fn, x='x', y='y', col=None, group=None, w=1100, h=800, size=2, smooth=True, point=True, jitter=False, boxplot=False, boxplot2=False, title=False, flip=False, se=False, density=False, line=False):
df=self.df
#import math, datetime
grdevices = importr('grDevices')
if not title:
title=fn.split("/")[-1]
grdevices.png(file=fn, width=w, height=h)
gp = ggplot2.ggplot(df)
pp = gp
if col and group:
pp+=ggplot2.aes_string(x=x, y=y,col=col,group=group)
elif col:
pp+=ggplot2.aes_string(x=x, y=y,col=col)
elif group:
pp+=ggplot2.aes_string(x=x, y=y,group=group)
else:
pp+=ggplot2.aes_string(x=x, y=y)
if boxplot:
if col:
pp+=ggplot2.geom_boxplot(ggplot2.aes_string(fill=col),color='blue')
else:
pp+=ggplot2.geom_boxplot(color='blue')
if point:
if jitter:
if col:
pp+=ggplot2.geom_point(ggplot2.aes_string(fill=col,col=col),size=size,position='jitter')
else:
pp+=ggplot2.geom_point(size=size,position='jitter')
else:
if col:
pp+=ggplot2.geom_point(ggplot2.aes_string(fill=col,col=col),size=size)
else:
pp+=ggplot2.geom_point(size=size)
if boxplot2:
if col:
pp+=ggplot2.geom_boxplot(ggplot2.aes_string(fill=col),color='blue',outlier_colour="NA")
else:
pp+=ggplot2.geom_boxplot(color='blue')
if smooth:
if smooth=='lm':
if col:
pp+=ggplot2.stat_smooth(ggplot2.aes_string(col=col),size=1,method='lm',se=se)
else:
pp+=ggplot2.stat_smooth(col='blue',size=1,method='lm',se=se)
else:
if col:
pp+=ggplot2.stat_smooth(ggplot2.aes_string(col=col),size=1,se=se)
else:
pp+=ggplot2.stat_smooth(col='blue',size=1,se=se)
if density:
pp+=ggplot2.geom_density(ggplot2.aes_string(x=x,y='..count..'))
if line:
pp+=ggplot2.geom_line(position='jitter')
pp+=ggplot2.opts(**{'title' : title, 'axis.text.x': ggplot2.theme_text(size=24), 'axis.text.y': ggplot2.theme_text(size=24,hjust=1)} )
#pp+=ggplot2.scale_colour_brewer(palette="Set1")
pp+=ggplot2.scale_colour_hue()
if flip:
pp+=ggplot2.coord_flip()
pp.plot()
grdevices.dev_off()
print ">> saved: "+fn
