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()