diff --git a/plot_lfclfc_scatter.py b/plot_lfclfc_scatter.py
index 9c17183ea5ff18c3bbc5ca27d30e4a6e377c4aab..b872063f59fa974f904245403ca76e2ba45a5c42 100755
--- a/plot_lfclfc_scatter.py
+++ b/plot_lfclfc_scatter.py
@@ -150,9 +150,21 @@ class Scatterplot:
line_style = {
"linewidth": 0.5, "color": "lightblue", "linestyle": "dashed"}
axis.axhline(y=1, **line_style)
+ axis.annotate(
+ f"y = 1", xy=(min(self.data.x)-1, 1), xycoords="data",
+ verticalalignment='bottom', size="x-small", color="lightblue")
axis.axhline(y=-1, **line_style)
+ axis.annotate(
+ f"y = -1", xy=(min(self.data.x)-1, -1), xycoords="data",
+ verticalalignment='top', size="x-small", color="lightblue")
axis.axvline(x=1, **line_style)
+ axis.annotate(
+ f"x = -1", xy=(-1, min(self.data.y)-1), xycoords="data",
+ horizontalalignment='right', rotation=90, size="x-small", color="lightblue")
axis.axvline(x=-1, **line_style)
+ axis.annotate(
+ f"x = 1", xy=(1, min(self.data.y)-1), xycoords="data",
+ horizontalalignment='left', rotation=90, size="x-small", color="lightblue")
# Number of genes beyond lfc thresholds, in each quadrant
# up_up = 100 * len(self.data.query(
# f"x > 1 & y > 1")) / len(self.data)
@@ -163,34 +175,34 @@ class Scatterplot:
# down_down = 100 * len(self.data.query(
# f"x < 1 & y < 1")) / len(self.data)
up_up = len(self.data.query(
- f"x > 1 & y > 1"))
+ "x > 1 & y > 1"))
up_down = len(self.data.query(
- f"x > 1 & y < 1"))
+ "x > 1 & y < -1"))
down_up = len(self.data.query(
- f"x < 1 & y > 1"))
+ "x < -1 & y > 1"))
down_down = len(self.data.query(
- f"x < 1 & y < 1"))
+ "x < -1 & y < -1"))
# axis.text(0.9, 0.9, f"{up_up}", transform = axis.transAxes)
# axis.text(0.9, 0.1, f"{up_down}", transform = axis.transAxes)
# axis.text(0.1, 0.9, f"{down_up}", transform = axis.transAxes)
# axis.text(0.1, 0.1, f"{down_down}", transform = axis.transAxes)
axis.annotate(
- f"{up_up}", xy=(0.95, 0.95), xycoords='axes fraction',
+ f"{up_up}", xy=(0.95, 0.95), xycoords="axes fraction",
size="x-small", color="lightblue",
horizontalalignment="right",
verticalalignment="top")
axis.annotate(
- f"{up_down}", xy=(0.95, 0.05), xycoords='axes fraction',
+ f"{up_down}", xy=(0.95, 0.05), xycoords="axes fraction",
size="x-small", color="lightblue",
horizontalalignment="right",
verticalalignment="bottom")
axis.annotate(
- f"{down_up}", xy=(0.05, 0.95), xycoords='axes fraction',
+ f"{down_up}", xy=(0.05, 0.95), xycoords="axes fraction",
size="x-small", color="lightblue",
horizontalalignment="left",
verticalalignment="top")
axis.annotate(
- f"{down_down}", xy=(0.05, 0.05), xycoords='axes fraction',
+ f"{down_down}", xy=(0.05, 0.05), xycoords="axes fraction",
size="x-small", color="lightblue",
horizontalalignment="left",
verticalalignment="bottom")
@@ -224,16 +236,6 @@ class Scatterplot:
equal_axes=True, tight=True)
-#########################################################
-# For better traceability, options and global variables #
-# should be stored as class attributes #
-#########################################################
-# class Globals(object):
-# """This object holds global variables."""
-# plot_diagonal = False
-# max_logfold = None
-
-
def main():
"""Main function of the program."""
print(" ".join(sys.argv))
@@ -304,39 +306,6 @@ def main():
help="Colour to use for the elements in the list given by option "
"--gene_list or --selector.")
# parser.add_argument(
- # "--label_size",
- # type=int,
- # help="Font size for axis labels",
- # default=24)
- # parser.add_argument(
- # "--hm_label_size",
- # type=int,
- # help="Font size for fold heatmap labels",
- # default=9)
- # parser.add_argument(
- # "--legend_size",
- # type=int,
- # help="Font size for legend labels",
- # default=9)
- # parser.add_argument(
- # "--marker_size",
- # type=int,
- # help="Size for markers on the plot",
- # default=4)
- # parser.add_argument(
- # "--tick_size",
- # type=int,
- # help="Font size for ticks",
- # default=18)
- # parser.add_argument(
- # "-x", "--x_axis",
- # help="Label for the x axis of the plot.",
- # required=True)
- # parser.add_argument(
- # "-y", "--y_axis",
- # help="Label for the y axis of the plot.",
- # required=True)
- # parser.add_argument(
# "-t", "--transform",
# help="log2, log10, or a linear scale to apply.",
# default=0)
@@ -347,8 +316,6 @@ def main():
args = parser.parse_args()
# if args.plot_diagonal:
# Globals.plot_diagonal = True
- # if args.max_logfold:
- # Globals.max_logfold = args.max_logfold
plot_data = Scatterplot(
args.x_input_data,
args.y_input_data,
@@ -365,10 +332,6 @@ def main():
# transform = int(args.transform)
if args.gene_list:
(list_name, base_gene_list) = get_gene_list(args.gene_list)
- # with open(args.gene_list, "r") as infile:
- # base_gene_list = [
- # strip_split(line)[0] for line in infile.readlines()
- # if line[0] != "#"]
else:
base_gene_list = []
if args.selector: