def test_get_logo_alt_input_type(self):
"""copes with positions with no values"""
data = [
{"A": 0.1, "C": 0.3, "G": 0.5, "T": 0.1},
{"A": 0.05, "C": 0.8, "G": 0.05, "T": 0.1},
{"A": 0.0, "C": 0.0, "G": 0.0, "T": 0.0},
{"A": 0.7, "C": 0.1, "G": 0.1, "T": 0.1},
{"A": 0.6, "C": 0.15, "G": 0.05, "T": 0.2},
]
d = get_logo(data)
data[-2] = {}
d = get_logo(data)
def test_get_logo_missing(self):
"""copes with positions with no values"""
data = [
[0.1, 0.3, 0.5, 0.1],
[0.05, 0.8, 0.05, 0.1],
[0, 0, 0, 0],
[0.7, 0.1, 0.1, 0.1],
[0.6, 0.15, 0.05, 0.2],
]
data = DictArrayTemplate(5, "ACGT").wrap(data)
d = get_logo(data)
def test_get_logo(self):
"""returns Drawable"""
data = [
[0.1, 0.3, 0.5, 0.1],
[0.25, 0.25, 0.25, 0.25],
[0.05, 0.8, 0.05, 0.1],
[0.7, 0.1, 0.1, 0.1],
[0.6, 0.15, 0.05, 0.2],
]
data = DictArrayTemplate(5, "ACGT").wrap(data)
d = get_logo(data)
def logo(self,
height=400,
width=800,
wrap=None,
ylim=None,
vspace=0.05,
colours=None):
"""returns a sequence logo Drawable"""
from cogent3.draw.drawable import get_domain
from cogent3.draw.logo import get_logo, get_mi_char_heights
assert 0 <= vspace <= 1, f"{vspace} not in range 0-1"
if ylim is None:
ylim = -numpy.log2(1 / self.shape[1]) * 1.1
if wrap is None:
mit = get_mi_char_heights(self)
logo = get_logo(mit,
height=height,
width=width,
ylim=ylim,
colours=colours)
return logo
wrap = min(wrap, self.shape[0])
rows, remainder = divmod(self.shape[0], wrap)
num_rows = rows + 1 if remainder else rows
axnum = 1
logo = None
xlim_text = {
"showarrow": False,
"text": "Position",
"x": None,
"xanchor": "center",
"xref": None,
"y": 0,
"yshift": 2,
"yanchor": "bottom",
"yref": None,
}
for i in range(0, self.shape[0], wrap):
axis = "axis" if axnum == 1 else f"axis{axnum}"
ydomain = get_domain(num_rows, axnum - 1, is_y=True, space=vspace)
segment = self[i:i + wrap, :]
mit = get_mi_char_heights(segment)
sublogo = get_logo(
mit,
height=height,
width=width,
axnum=axnum,
ydomain=ydomain,
ylim=ylim,
colours=colours,
)
xtick_vals = [j for j in range(0, segment.shape[0], 20)]
xtick_text = [f"{i + j}" for j in range(0, segment.shape[0], 20)]
sublogo.layout[f"x{axis}"].showticklabels = False
sublogo.layout[f"x{axis}"].domain = [0, segment.shape[0] / wrap]
# place the row limit x-coord
xtext = xlim_text.copy()
xtext["text"] = f"{i + segment.shape[0]}"
xtext["x"] = segment.shape[0] + 1
xtext["xref"] = f"x{'' if axnum == 1 else axnum}"
xtext["yref"] = f"y{'' if axnum == 1 else axnum}"
sublogo.layout.annotations = [xtext]
if logo is None:
logo = sublogo
else:
logo.layout.shapes.extend(sublogo.layout.shapes)
logo.layout.annotations.extend(sublogo.layout.annotations)
logo.layout[f"x{axis}"] = sublogo.layout[f"x{axis}"]
logo.layout[f"y{axis}"] = sublogo.layout[f"y{axis}"]
axnum += 1
return logo