From 3ddac00d113a40a5802b8f326889860345f160f0 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Thu, 6 Jun 2019 11:58:12 +0200
Subject: [PATCH] Made lfc-lfc plotting specificities optional.
---
plot_scatterplot.py | 231 +++++++++++++++++++++++---------------------
1 file changed, 123 insertions(+), 108 deletions(-)
diff --git a/plot_scatterplot.py b/plot_scatterplot.py
index b4d4378..94bb79b 100755
--- a/plot_scatterplot.py
+++ b/plot_scatterplot.py
@@ -152,9 +152,11 @@ class Scatterplot:
if gene_id in chose_from]
return [gene_id for gene_id in self.data.query(selector).index]
- def plot_maker(self, 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*."""
+ belonging to a group defined by *grouping*.
+ If *annotate_folds* is True, lines indicating 2-fold thresholds
+ will be added to the plot, as well as counts in each quadrants."""
def plotting_function():
"""Generates the scatterplot, returns its legend so that
*save_plot* can include it in the bounding box."""
@@ -173,110 +175,111 @@ class Scatterplot:
return None
else:
raise
- # Lines indicating 2-fold threshold.
- # Assumes the data are in log2 fold changes
- line_style = {
- "linewidth": 0.5, "color": "0.5", "linestyle": "dashed"}
- if "x_range" in kwargs:
- (x_annot_loc, _) = kwargs["x_range"]
- else:
- x_annot_loc = min(self.data.x)
- if "y_range" in kwargs:
- (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)
- up_up = self.data.query(
- "x > 1 & y > 1")
- up_down = self.data.query(
- "x > 1 & y < -1")
- down_up = self.data.query(
- "x < -1 & y > 1")
- down_down = self.data.query(
- "x < -1 & y < -1")
- if isinstance(grouping, (list, tuple)):
- try:
- (_, colour) = group2colour
- except (ValueError, TypeError):
- colour = "black"
- select_ingroup = pd.Index(grouping).intersection
- ingroup_up_up = " (\\textcolor{%s}{%d})" % (
- colour,
- len(up_up.loc[select_ingroup(up_up.index)]),)
- ingroup_up_down = " (\\textcolor{%s}{%d})" % (
- colour,
- len(up_down.loc[select_ingroup(up_down.index)]))
- ingroup_down_up = " (\\textcolor{%s}{%d})" % (
- colour,
- len(down_up.loc[select_ingroup(down_up.index)]))
- ingroup_down_down = " (\\textcolor{%s}{%d})" % (
- colour,
- len(down_down.loc[select_ingroup(down_down.index)]))
- else:
- ingroup_up_up = ""
- ingroup_up_down = ""
- ingroup_down_up = ""
- ingroup_down_down = ""
- axis.annotate(
- 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")
+ if annotate_folds:
+ # Lines indicating 2-fold threshold.
+ # Assumes the data are in log2 fold changes
+ line_style = {
+ "linewidth": 0.5, "color": "0.5", "linestyle": "dashed"}
+ if "x_range" in kwargs:
+ (x_annot_loc, _) = kwargs["x_range"]
+ else:
+ x_annot_loc = min(self.data.x)
+ if "y_range" in kwargs:
+ (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)
+ up_up = self.data.query(
+ "x > 1 & y > 1")
+ up_down = self.data.query(
+ "x > 1 & y < -1")
+ down_up = self.data.query(
+ "x < -1 & y > 1")
+ down_down = self.data.query(
+ "x < -1 & y < -1")
+ if isinstance(grouping, (list, tuple)):
+ try:
+ (_, colour) = group2colour
+ except (ValueError, TypeError):
+ colour = "black"
+ select_ingroup = pd.Index(grouping).intersection
+ ingroup_up_up = " (\\textcolor{%s}{%d})" % (
+ colour,
+ len(up_up.loc[select_ingroup(up_up.index)]),)
+ ingroup_up_down = " (\\textcolor{%s}{%d})" % (
+ colour,
+ len(up_down.loc[select_ingroup(up_down.index)]))
+ ingroup_down_up = " (\\textcolor{%s}{%d})" % (
+ colour,
+ len(down_up.loc[select_ingroup(down_up.index)]))
+ ingroup_down_down = " (\\textcolor{%s}{%d})" % (
+ colour,
+ len(down_down.loc[select_ingroup(down_down.index)]))
+ else:
+ ingroup_up_up = ""
+ ingroup_up_down = ""
+ ingroup_down_up = ""
+ ingroup_down_down = ""
+ axis.annotate(
+ 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")
axis.set_xlabel(self.x_label, fontsize=17)
axis.set_ylabel(self.y_label, fontsize=17)
# This doesn't work with plt.axis("equal")
@@ -307,7 +310,7 @@ class Scatterplot:
return plotting_function
def save_plot(self, outfile,
- grouping=None, group2colour=None,
+ annotate_folds=True, grouping=None, group2colour=None,
**kwargs):
"""Creates the plotting function and transmits it for execution
to the function that really does the saving."""
@@ -318,10 +321,14 @@ class Scatterplot:
# equal_axes = False
# else:
# equal_axes = True
- equal_axes = True
+ if annotate_folds:
+ equal_axes = True
+ else:
+ equal_axes = False
save_plot(
outfile,
self.plot_maker(
+ annotate_folds,
grouping=grouping, group2colour=group2colour, **kwargs),
equal_axes=equal_axes,
tight=True)
@@ -407,6 +414,12 @@ def main():
# "-t", "--transform",
# help="log2, log10, or a linear scale to apply.",
# default=0)
+ parser.add_argument(
+ "--not_foldchanges",
+ help="Use this option to inactivate plotting options for "
+ "log2FoldChange.",
+ default=False,
+ action="store_true")
parser.add_argument(
"--plot_regression",
help="Use this option to plot the regression line.",
@@ -476,6 +489,7 @@ def main():
plot_data.save_plot(
# args.x_axis, args.y_axis,
out_pdf,
+ annotate_folds=not args.not_foldchanges,
grouping=gene_list, group2colour=(list_name, args.colour),
x_range=args.data_range,
y_range=args.data_range,
@@ -489,6 +503,7 @@ def main():
plot_data.save_plot(
# args.x_axis, args.y_axis,
out_pdf,
+ annotate_folds=not args.not_foldchanges,
x_range=args.data_range,
y_range=args.data_range,
regression=args.plot_regression)
--
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