def plot_combo(combo, outname, mids):
ggdat = {"data": combo, "outname": outname, "mids": mids}
command = """
outname = jdata$outname
mids = jdata$mids
# labs = c("Gene", "Repeat_content")
# names(labs) = c("Genes", "Repeats")
scale = 2
pdf(outname, height=10*4*scale, width=20*scale)
aplot = ggplot(data = data, aes(plotpos, true_density)) +
geom_point() +
xlab("Chromosome") +
ylab("Features per basepair") + ## y label from qqman::qq
#scale_color_manual(values = c(gray(0.5), gray(0))) + ## instead of colors, go for gray
ggtitle("Chromosome-wide feature density") +
theme_bw() +
#scale_y_continuous(breaks=seq(from=min(data$true_density), to=max(data$true_density), length.out=3)) +
facet_grid(Feature~., scales="free_y") +
scale_x_continuous(breaks = mids$mid, labels = mids$Scaffold_number) + ## add new x labels
theme(text = element_text(size=32))
print(aplot)
dev.off()
# facet_grid(Feature~., scales="free_y", labeller=labeller(Feature=labs)) +
# facet_wrap(.~NAME, ncol = 2) +
# guides(colour=FALSE) + ## remove legend
"""
pygg.ggplot(ggdat, command)
def testLibs(self):
p = pygg.ggplot('diamonds', pygg.aes(x='carat', y='price'))
p += pygg.geom_point()
tmpfile = tempfile.NamedTemporaryFile(suffix='.pdf').name
pygg.ggsave(tmpfile, p, data=None, libs=['grid'], quiet=True)
self.assertTrue(os.path.exists(tmpfile))
self.assertTrue(os.path.getsize(tmpfile) > 0)
def testLibs(self):
p = pygg.ggplot('diamonds', pygg.aes(x='carat', y='price'))
p += pygg.geom_point()
tmpfile = tempfile.NamedTemporaryFile(suffix='.pdf').name
pygg.ggsave(tmpfile, p, data=None, libs=['grid'], quiet=True)
self.assertTrue(os.path.exists(tmpfile))
self.assertTrue(os.path.getsize(tmpfile) > 0)
def testBasicDataggplot(self):
data = [dict(x=x, y=y) for x, y in zip(range(10), range(10))]
p = pygg.ggplot(data, pygg.aes(x='x', y='y'))
p += pygg.geom_point()
p += pygg.geom_smooth()
p += pygg.ggtitle(pygg.esc('Test title'))
self.check_ggsave(p)
def testBasicDataggplot(self):
data = [dict(x=x, y=y) for x, y in zip(range(10), range(10))]
p = pygg.ggplot(data, pygg.aes(x='x', y='y'))
p += pygg.geom_point()
p += pygg.geom_smooth()
p += pygg.ggtitle(pygg.esc('Test title'))
self.check_ggsave(p)
def plot_combo(combo, outname, mids):
ggdat = {"data": combo, "outname": outname, "mids": mids}
command = """
library(plyr)
outname = jdata$outname
mids = jdata$mids
# labs = c("Gene", "Repeat_content")
# names(labs) = c("Genes", "Repeats")
scale = 2
print(str(data$Feature))
print(levels(factor(data$Feature)))
temp = factor(data$Feature)
print(str(temp))
print(levels(factor(temp)))
temp = revalue(temp, c("Low_complexity" = "Low\ncomp-\nlexity", "Simple_repeat" = "Simple\nrepeat"))
print(str(temp))
print(levels(factor(temp)))
data$Feature = as.character(temp)
print(str(data$Feature))
print(levels(factor(data$Feature)))
lf_feature = levels(factor(data$Feature))
dummy = data.frame(Feature=lf_feature, true_density = 0, plotpos = min(data$plotpos))
pdf(outname, height=3*4.6*scale, width=20*scale)
aplot = ggplot(data = data, aes(plotpos, true_density)) +
geom_point() +
xlab("Chromosome") +
ylab("Feature bases per genome base") + ## y label from qqman::qq
#scale_color_manual(values = c(gray(0.5), gray(0))) + ## instead of colors, go for gray
#ggtitle("Chromosome-wide feature density") +
theme_bw() +
scale_y_continuous(labels = function(x) sprintf("%.5f", x)) +
#scale_y_continuous(labels = function(x) format(x, scientific = TRUE)) +
#scale_y_continuous(breaks=seq(from=min(data$true_density), to=max(data$true_density), length.out=3)) +
facet_grid(Feature~., scales="free_y") +
scale_x_continuous(breaks = mids$mid, labels = mids$Scaffold_number) + ## add new x labels
geom_blank(data=dummy) +
theme(text = element_text(size=48), panel.spacing = unit(1.8, "lines"), plot.margin = unit(c(.5,.5,.5,.5), "cm"))
print(aplot)
dev.off()
# facet_grid(Feature~., scales="free_y", labeller=labeller(Feature=labs)) +
# facet_wrap(.~NAME, ncol = 2) +
# guides(colour=FALSE) + ## remove legend
"""
pygg.ggplot(ggdat, command)
def testPandasDFggplot(self):
data = pandas.read_csv(StringIO.StringIO(IRIS_DATA_CSV))
self.assertIsInstance(data, pandas.DataFrame)
p = pygg.ggplot(
data, pygg.aes(x='SepalLength', y='PetalLength', color='Name'))
p += pygg.geom_point()
p += pygg.geom_smooth()
p += pygg.ggtitle(pygg.esc('Test title'))
self.check_ggsave(p)
def testPandasDF(self):
data = pandas.read_csv(StringIO.StringIO(IRIS_DATA_CSV))
self.assertIsInstance(data, pandas.DataFrame)
p = pygg.ggplot('data',
pygg.aes(x='SepalLength', y='PetalLength', color='Name'))
p += pygg.geom_point()
p += pygg.geom_smooth()
p += pygg.ggtitle(pygg.esc('Test title'))
self.check_ggsave(p, data)
def testE2E(self):
"""Test end-to-end creation of figures with outputs to pdf and png"""
p = pygg.ggplot('diamonds', pygg.aes(x='carat', y='price', color='clarity'))
p += pygg.geom_point(alpha=0.5, size = .75)
p += pygg.scale_x_log10()
p += pygg.theme_bw()
self.check_ggsave(p, None, ext=".pdf")
self.check_ggsave(p, None, ext=".png")
self.check_ggsave(p, None, ext=".jpg")
def testE2E(self):
"""Test end-to-end creation of figures with outputs to pdf and png"""
p = pygg.ggplot('diamonds',
pygg.aes(x='carat', y='price', color='clarity'))
p += pygg.geom_point(alpha=0.5, size=.75)
p += pygg.scale_x_log10()
p += pygg.theme_bw()
self.check_ggsave(p, None, ext=".pdf")
self.check_ggsave(p, None, ext=".png")
self.check_ggsave(p, None, ext=".jpg")
def testIPython(self):
"""Test that gg_ipython returns a IPython formatted Image"""
p = pygg.ggplot('diamonds', pygg.aes(x='carat', y='price'))
p += pygg.geom_point()
img = pygg.gg_ipython(p, data=None)
self.assertIsNotNone(img.data)
self.assertEqual(img.format, "jpeg")
self.assertEqual(img.width, pygg.IPYTHON_IMAGE_SIZE)
self.assertEqual(img.height, pygg.IPYTHON_IMAGE_SIZE)
img = pygg.gg_ipython(p, data=None, width=600, height=400)
self.assertEqual(img.width, 600)
self.assertEqual(img.height, 400)
img = pygg.gg_ipython(p, data=None, width=600)
self.assertEqual(img.width, 600)
self.assertEqual(img.height, 600)
def testIPython(self):
"""Test that gg_ipython returns a IPython formatted Image"""
p = pygg.ggplot('diamonds', pygg.aes(x='carat', y='price'))
p += pygg.geom_point()
img = pygg.gg_ipython(p, data=None)
self.assertIsNotNone(img.data)
self.assertEqual(img.format, "jpeg")
self.assertEqual(img.width, pygg.IPYTHON_IMAGE_SIZE)
self.assertEqual(img.height, pygg.IPYTHON_IMAGE_SIZE)
img = pygg.gg_ipython(p, data=None, width=600, height=400)
self.assertEqual(img.width, 600)
self.assertEqual(img.height, 400)
img = pygg.gg_ipython(p, data=None, width=600)
self.assertEqual(img.width, 600)
self.assertEqual(img.height, 600)
def testNativeRDataset(self):
p = pygg.ggplot('diamonds', pygg.aes(x='carat', y='carat')) + pygg.geom_point()
self.check_ggsave(p, None)
def testLimits(self):
p = pygg.ggplot('diamonds',
pygg.aes(x='carat', y='price', color='clarity'))
p += pygg.geom_point(alpha=0.5, size=.75)
p += pygg.scale_x_log10(limits=[1, 2])
self.check_ggsave(p, None)
#!/usr/bin/env python3
import pandas as pd
import pygg
import json
data = pd.read_csv("aeds_prot.txt", sep="\t", header=0)
data = data.sort_values("aed")
datalen = data.shape[0]
data["frac"] = [float(x) / datalen for x in range(data.shape[0])]
print(data)
jdata = {"data": data}
ggc = """
a = ggplot(data=data, aes(aed, frac)) + geom_line() +
geom_vline(xintercept=.5, linetype="dashed") +
theme_bw() +
labs(y="Cumulative proportion of all transcripts", x="AED", title="Annotation AED scores")
pdf("aeds4_final.pdf", height=3, width=4)
print(a)
dev.off()
"""
pygg.ggplot(jdata, ggc)
def testBadGGPlotFails(self):
p = pygg.ggplot('diamonds', pygg.aes(x='MISSING')) + pygg.geom_point()
with self.assertRaises(ValueError):
tmpfile = tempfile.NamedTemporaryFile(suffix=".png").name
pygg.ggsave(tmpfile, p, data=None, quiet=True)
def testFacets2(self):
p = pygg.ggplot('diamonds', pygg.aes(x='carat', y='price'))
p += pygg.geom_point()
p += pygg.facet_wrap("~clarity")
self.check_ggsave(p, None)
def testLimits(self):
p = pygg.ggplot('diamonds', pygg.aes(x='carat', y='price', color='clarity'))
p += pygg.geom_point(alpha=0.5, size = .75)
p += pygg.scale_x_log10(limits=[1, 2])
self.check_ggsave(p, None)
def testFacets2(self):
p = pygg.ggplot('diamonds', pygg.aes(x='carat', y='price'))
p += pygg.geom_point()
p += pygg.facet_wrap("~clarity")
self.check_ggsave(p, None)
def testNativeRDataset(self):
p = pygg.ggplot('diamonds', pygg.aes(x='carat',
y='carat')) + pygg.geom_point()
self.check_ggsave(p, None)
def plot_manhat(combo,
outname,
mids,
val_col,
title="Manhattan plot",
dims=(20.0, 10.0),
scale=2,
text_size=32,
xname="Chromosome",
yname="Value",
color_col=None,
facet_col=None):
ggdat = {
"data": combo,
"outname": outname,
"mids": mids,
"title": title,
"dims": dims,
"scale": scale,
"text_size": text_size,
"xname": xname,
"yname": yname,
"color_col": color_col,
"facet_col": facet_col
}
preamble = """
outname = jdata$outname
mids = jdata$mids
scale = jdata$scale
pdf(outname, height=jdata$dims[2]*scale, width=jdata$dims[1]*scale)
"""
if color_col:
aes = "aes(plotpos, " + val_col + ", color = " + color_col + ")"
else:
aes = "aes(plotpos, " + val_col + ")"
plot_command = """
aplot = ggplot(data = data, """ + aes + """) +
geom_point() +
xlab(jdata$xname) +
ylab(jdata$yname) + ## y label from qqman::qq
#scale_color_manual(values = c(gray(0.5), gray(0))) + ## instead of colors, go for gray
ggtitle(jdata$title) +
theme_bw() +
#scale_y_continuous(breaks=seq(from=min(data$""" + val_col + """), to=max(data$""" + val_col + """), length.out=3)) +
scale_x_continuous(breaks = mids$mid, labels = mids$Scaffold_number) + ## add new x labels
theme(text = element_text(size=jdata$text_size))"""
if facet_col:
plot_command = plot_command + """ +
facet_grid(""" + facet_col + """~., scales="free_y")"""
plot_command = plot_command + "\n"
ending = """
print(aplot)
dev.off()
# facet_grid(Feature~., scales="free_y", labeller=labeller(Feature=labs)) +
# facet_wrap(.~NAME, ncol = 2) +
# guides(colour=FALSE) + ## remove legend
"""
command = preamble + plot_command + ending
pygg.ggplot(ggdat, command)
def testBadGGPlotFails(self):
p = pygg.ggplot('diamonds', pygg.aes(x='MISSING')) + pygg.geom_point()
with self.assertRaises(ValueError):
tmpfile = tempfile.NamedTemporaryFile(suffix=".png").name
pygg.ggsave(tmpfile, p, data=None, quiet=True)
