def __init__(self, *args, **kwargs):
super(ExpressionDisplay, self).__init__(*args, **kwargs)
svg = self.svg = canvas.SVGCanvasWidget()
svg.add_style("background-color", "cornsilk")
svg.svg_width = 550
svg.svg_height = 550
svg.watch_event = "click mousemove"
svg.default_event_callback = self.svg_callback
cc = self.color_chooser = color_widget.ColorChooser()
#cc.svg.visible = False # default
set_visibility(cc.svg, False)
tdd = self.transform_dropdown = widgets.Dropdown(
options=TRANSFORM_TEXTS,
value=NO_TRANSFORM
)
tdd.on_trait_change(self.draw_click, "value")
tdd.layout.width = "100px"
self.title_html = widgets.HTML("Expression Heat Map")
self.text_assembly = self.make_text_displays()
self.match_assembly = self.make_match_assembly()
self.genes_assembly = self.make_genes_assembly(tdd)
self.info_area = widgets.Textarea(description="status")
self.assembly = widgets.VBox(children=[self.title_html,
self.text_assembly,
self.svg,
self.color_chooser.svg,
self.match_assembly,
self.genes_assembly,
self.info_area])
self.dx = 10
self.dy = 2
self.data_heat_map = None
self.display_heat_map = None
self.row = self.col = None
self.drawing = False
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, *args, **kwargs):
super(ColorPicker, self).__init__(*args, **kwargs)
svg = self.svg = canvas.SVGCanvasWidget()
svg.svg_height = self.palette_side + 2 * self.dy
svg.svg_width = self.palette_side
svg.set_view_box(0, 0, svg.svg_width, svg.svg_height)
svg.watch_event = "click"
svg.default_event_callback = self.svg_callback
#self.color = color_scale.color(color_scale.color64(0, 0))
self.on_trait_change(self.show_color_choice, "color")
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
def __init__(self, *args, **kwargs):
super(ColorChooser, self).__init__(*args, **kwargs)
svg = self.svg = canvas.SVGCanvasWidget()
svg.svg_width = self.margin * 2 + self.palette_side
middle = self.palette_side + self.histogram_region + self.bar_region
svg.svg_height = self.margin * 2 + middle
svg.set_view_box(- self.margin,
- self.margin,
self.palette_side + 2 * self.margin,
middle + 2 * self.margin)
self.scale = color_scale.ColorInterpolator(minvalue=-3.33323, maxvalue=1.3432)
svg.watch_event = "click mousemove"
svg.default_event_callback = self.svg_callback
self.drag_color = None
self.drag_circle = None
self.histogram = None
def assemble(self):
guide = self.guide
wigs = self.wigs
vertical = []
for wig in wigs:
svg = wig.svg = canvas.SVGCanvasWidget()
vertical.append(svg)
svg.width = self.width
svg.height = self.height
svg.set_view_box(0, 0, self.width, self.height)
svg.add_style("background-color", "cyan")
traitlets.link((guide, "start_position"), (wig, "start_position"))
traitlets.link((guide, "end_position"), (wig, "end_position"))
vertical.append(self.guide.assembly)
self.assembly = widgets.VBox(children=vertical)
wig.on_trait_change(self.draw, "start_position")
self.assembled = True
def canvas(self):
svg = canvas.SVGCanvasWidget()
svg.add_style("background-color", "cyan")
svg.width = 500
svg.height = 10
return svg