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Commit e332b282 authored by Blaise Li's avatar Blaise Li
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Moved optional plotting to static methods.

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with 90 additions and 58 deletions
plot_scatterplot.py
+ 90
− 58
View file @ e332b282
......@@ -83,6 +83,85 @@ class Scatterplot:
Intended to be used with *DataFrame.apply*."""
return "_".join(map(str, row.values))
@staticmethod
def put_quadrants(axis, x_annot_loc, y_annot_loc, line_style):
"""Delineate quadrants of absolute fold changes over 2.
*axis* is the :class:`matplotlib.axes.Axes` on which to work.
*x_annot_loc* and *y_annot_loc* are the position at which to annotate
the lines delineating the quadrants.
This works through side effects on *axis*.
"""
axis.axhline(y=1, **line_style)
axis.annotate(
f"y = 1", xy=(x_annot_loc, 1), xycoords="data",
horizontalalignment='left',
verticalalignment='bottom',
size="x-small",
color=line_style["color"])
axis.axhline(y=-1, **line_style)
axis.annotate(
f"y = -1", xy=(x_annot_loc, -1), xycoords="data",
horizontalalignment='left',
verticalalignment='top',
size="x-small",
color=line_style["color"])
axis.axvline(x=1, **line_style)
axis.annotate(
f"x = -1", xy=(-1, y_annot_loc), xycoords="data",
horizontalalignment='right',
verticalalignment='bottom',
rotation=90, size="x-small",
color=line_style["color"])
axis.axvline(x=-1, **line_style)
axis.annotate(
f"x = 1", xy=(1, y_annot_loc), xycoords="data",
horizontalalignment='left',
verticalalignment='bottom',
rotation=90, size="x-small",
color=line_style["color"])
@staticmethod
def write_quadrant_counts(axis,
annot_up_up, annot_up_down,
annot_down_up, annot_down_down,
text_color):
"""Annotate quadrants of absolute fold changes over 2.
*axis* is the :class:`matplotlib.axes.Axes` on which to work.
*annot_up_up*, *annot_up_down*, *annot_down_up* and *annot_down_down*
are the annotations to put in each quadrant.
This works through side effects on *axis*.
"""
axis.annotate(
annot_up_up,
xy=(0.95, 0.95), xycoords="axes fraction",
size="x-small", color=text_color,
horizontalalignment="right",
verticalalignment="top")
axis.annotate(
annot_up_down,
xy=(0.95, 0.05), xycoords="axes fraction",
size="x-small", color=text_color,
horizontalalignment="right",
verticalalignment="bottom")
axis.annotate(
annot_down_up,
xy=(0.05, 0.95), xycoords="axes fraction",
size="x-small", color=text_color,
horizontalalignment="left",
verticalalignment="top")
axis.annotate(
annot_down_down,
xy=(0.05, 0.05), xycoords="axes fraction",
size="x-small", color=text_color,
horizontalalignment="left",
verticalalignment="bottom")
def __init__(self,
x_input_file,
y_input_file,
......@@ -152,7 +231,11 @@ class Scatterplot:
if gene_id in chose_from]
return [gene_id for gene_id in self.data.query(selector).index]
def plot_maker(self, annotate_folds=True, grouping=None, group2colour=None, **kwargs):
def plot_maker(self,
annotate_folds=True,
grouping=None,
group2colour=None,
**kwargs):
"""Builds a plotting function that can colour dots based on them
belonging to a group defined by *grouping*.
If *annotate_folds* is True, lines indicating 2-fold thresholds
......@@ -188,43 +271,9 @@ class Scatterplot:
(y_annot_loc, _) = kwargs["y_range"]
else:
y_annot_loc = min(self.data.y)
axis.axhline(y=1, **line_style)
axis.annotate(
f"y = 1", xy=(x_annot_loc, 1), xycoords="data",
horizontalalignment='left',
verticalalignment='bottom',
size="x-small",
color=line_style["color"])
axis.axhline(y=-1, **line_style)
axis.annotate(
f"y = -1", xy=(x_annot_loc, -1), xycoords="data",
horizontalalignment='left',
verticalalignment='top',
size="x-small",
color=line_style["color"])
axis.axvline(x=1, **line_style)
axis.annotate(
f"x = -1", xy=(-1, y_annot_loc), xycoords="data",
horizontalalignment='right',
verticalalignment='bottom',
rotation=90, size="x-small",
color=line_style["color"])
axis.axvline(x=-1, **line_style)
axis.annotate(
f"x = 1", xy=(1, y_annot_loc), xycoords="data",
horizontalalignment='left',
verticalalignment='bottom',
rotation=90, size="x-small",
color=line_style["color"])
# Number of genes beyond lfc thresholds, in each quadrant
# up_up = 100 * len(self.data.query(
# f"x > 1 & y > 1")) / len(self.data)
# up_down = 100 * len(self.data.query(
# f"x > 1 & y < 1")) / len(self.data)
# down_up = 100 * len(self.data.query(
# f"x < 1 & y > 1")) / len(self.data)
# down_down = 100 * len(self.data.query(
# f"x < 1 & y < 1")) / len(self.data)
Scatterplot.put_quadrants(
axis, x_annot_loc, y_annot_loc, line_style)
# Genes beyond lfc thresholds, in each quadrant
up_up = self.data.query(
"x > 1 & y > 1")
up_down = self.data.query(
......@@ -256,30 +305,13 @@ class Scatterplot:
ingroup_up_down = ""
ingroup_down_up = ""
ingroup_down_down = ""
axis.annotate(
Scatterplot.write_quadrant_counts(
axis,
f"{len(up_up)}{ingroup_up_up}",
xy=(0.95, 0.95), xycoords="axes fraction",
size="x-small", color=line_style["color"],
horizontalalignment="right",
verticalalignment="top")
axis.annotate(
f"{len(up_down)}{ingroup_up_down}",
xy=(0.95, 0.05), xycoords="axes fraction",
size="x-small", color=line_style["color"],
horizontalalignment="right",
verticalalignment="bottom")
axis.annotate(
f"{len(down_up)}{ingroup_down_up}",
xy=(0.05, 0.95), xycoords="axes fraction",
size="x-small", color=line_style["color"],
horizontalalignment="left",
verticalalignment="top")
axis.annotate(
f"{len(down_down)}{ingroup_down_down}",
xy=(0.05, 0.05), xycoords="axes fraction",
size="x-small", color=line_style["color"],
horizontalalignment="left",
verticalalignment="bottom")
line_style["color"])
axis.set_xlabel(self.x_label, fontsize=17)
axis.set_ylabel(self.y_label, fontsize=17)
# This doesn't work with plt.axis("equal")
......
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