diff --git a/plot_scatterplot.py b/plot_scatterplot.py
index 94bb79bad09b1462cf5738944fe594feb4e376f7..9149ae820f8b5197a13383c1309fa04fe56342f4 100755
--- a/plot_scatterplot.py
+++ b/plot_scatterplot.py
@@ -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")