def test0():
import pprint
import gtf_format
from jp_svg_canvas import canvas
canvas.load_javascript_support()
GB = GenomeBar()
f = open("genes.gtf")
print ("reading file")
if 0:
L = list(gtf_format.gtf_lines_to_dicts(f))
L = [d for d in L if d.get("feature") == "exon"]
else:
D = gtf_format.GTFData()
D.load(f)
GF = D.get_gene_features(["tmc6"])
#pprint.pprint(sorted(D.gene_id_to_dicts.keys()))
pprint.pprint(GF)
L = GF["tmc6"]
print "loading", len(L)
for feature in L:
atts = feature["attribute"]
kind = feature.get("feature")
gene_id = atts.get("gene_id")
if kind == "exon" and gene_id:
name = gene_id + str(feature["start"])
GB.add_feature(name, feature)
svg = canvas.SVGCanvasWidget()
GB.fit(svg)
print ("drawing")
GB.draw(svg)
print ("done")
return svg
def test0():
import pprint
import gtf_format
from jp_svg_canvas import canvas
canvas.load_javascript_support()
GB = GenomeBar()
f = open("genes.gtf")
print("reading file")
if 0:
L = list(gtf_format.gtf_lines_to_dicts(f))
L = [d for d in L if d.get("feature") == "exon"]
else:
D = gtf_format.GTFData()
D.load(f)
GF = D.get_gene_features(["tmc6"])
#pprint.pprint(sorted(D.gene_id_to_dicts.keys()))
pprint.pprint(GF)
L = GF["tmc6"]
print("loading", len(L))
for feature in L:
atts = feature["attribute"]
kind = feature.get("feature")
gene_id = atts.get("gene_id")
if kind == "exon" and gene_id:
name = gene_id + str(feature["start"])
GB.add_feature(name, feature)
svg = canvas.SVGCanvasWidget()
GB.fit(svg)
print("drawing")
GB.draw(svg)
print("done")
return svg
def __init__(self, target_canvas, scaling=1.0, x_scaling=None, y_scaling=None,
x_offset=0.0, y_offset=0.0):
canvas.load_javascript_support()
self.x_scaling = self.y_scaling = scaling
if x_scaling is not None:
self.x_scaling = x_scaling
if y_scaling is not None:
self.y_scaling = y_scaling
self.x_offset = x_offset
self.y_offset = y_offset
self.target = target_canvas
self.prefix_to_names = {}
self.prefix_to_count = {}
def canvas_test(filename="ex2.wig.gz", width=500, height=100):
from jp_svg_canvas import canvas
canvas.load_javascript_support()
svg = canvas.SVGCanvasWidget()
svg.add_style("background-color", "cyan")
svg.svg_width = width
svg.svg_height = height
svg.set_view_box(0, 0, width, height)
W = WigData()
print ("loading: " + repr(filename))
W.load_filename(filename)
print ("loaded " + repr(W.numelts) + " max " + repr(W.maxheight))
W.draw(svg, 3010000, 3010200, width, height)
return (svg, W)
def widget(self):
from jp_svg_canvas import canvas
canvas.load_javascript_support(True)
svg_canvas = canvas.SVGCanvasWidget()
self.plot_all(svg_canvas)
svg_canvas.send_commands()
display(svg_canvas)
# fit must happen after display.
svg_canvas.fit()
svg_canvas.send_commands()
canvas_side = len(self.dataset.feature_names) * self.side
canvas_side = max(canvas_side, 500)
svg_canvas.width = canvas_side
svg_canvas.height = canvas_side
return svg_canvas
import numpy as np
from numpy.linalg import norm
from jp_svg_canvas import canvas, cartesian_svg
from jp_gene_viz import proxy_html5_canvas
from jp_gene_viz import js_proxy
import contourist.lasso
from threading import Timer
canvas.load_javascript_support()
import ipywidgets as widgets
from IPython.display import display
SLIDE = 'SLIDE'
SLIDE_x = 'SLIDE_x'
SLIDE_y = 'SLIDE_y'
TSNE_x = 'TSNE_x'
TSNE_y = 'TSNE_y'
INDICATOR = 'INDICATOR'
NAME = "NAME"
#SLIDE_SIZE = 40
TSNE_RADIUS = 11
BACKGROUND_COLOR = "#FFFFDD"
def canvas_doodle(xmin, ymin, xmax, ymax, html_width=500, html_height=None, margin=50):
canvas = proxy_html5_canvas.HTML5CanvasProxy()
result = cartesian_svg.doodle(xmin, ymin, xmax, ymax, html_width, html_height, margin, svg=canvas)
result.buffered = True
return result
def load_javascript_support(verbose=False):
canvas.load_javascript_support()
js_proxy.load_javascript_support()
