From 7f77571e7258163579d48bf68691dd39ef2f953f Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Wed, 27 Jan 2021 16:41:15 +0100
Subject: [PATCH] src/visu/__main__.py: add parameter ylim
---
src/visu/__main__.py | 10 +++++++---
1 file changed, 7 insertions(+), 3 deletions(-)
diff --git a/src/visu/__main__.py b/src/visu/__main__.py
index bc53640..a72845d 100644
--- a/src/visu/__main__.py
+++ b/src/visu/__main__.py
@@ -10,7 +10,7 @@ gene regions from ChIP-seq experiment.
from .figure_maker import create_figure
import lazyparser as lp
from pathlib import Path
-from typing import List
+from typing import List, Optional
@lp.parse(design='file', region_beds='file',
@@ -21,7 +21,7 @@ def launcher(design: str, bw_folder: str, region_beds: List[str],
figure_type: str = 'metagene', norm: str = 'None',
show_replicate: str = 'y', environment: List[int] = (0, 0),
border_names: List[str] = ('', ''),
- output: str = '.') -> None:
+ output: str = '.', ylim: List[float] = (None, None)) -> None:
"""
Create A metagene or a barplot figure from bigwig file on regions defined \
in the bed file provided with 'region_bed' parameter.
@@ -47,7 +47,11 @@ def launcher(design: str, bw_folder: str, region_beds: List[str],
the number of bin used to represent those surrounding regions.
:param border_names: The name of the borders
:param output: Folder where the results will be created
+ :param ylim: The y-axis range (default None)
"""
+ if ylim[0] is not None and (len(ylim) != 2 or ylim[0] >= ylim[1]):
+ raise ValueError("The ylim must have two values and the first value "
+ "must be lower to the second value")
if environment[0] < 0 or environment[1] < 0 or \
environment[0] < environment[1]:
raise ValueError(f"The two values given with --environment must "
@@ -62,7 +66,7 @@ def launcher(design: str, bw_folder: str, region_beds: List[str],
reg_beds = [Path(p) for p in region_beds]
create_figure(Path(design), Path(bw_folder), reg_beds,
region_names, nb_bin, figure_type, norm, show_rep,
- environment, border_names, Path(output))
+ environment, border_names, Path(output), ylim)
launcher()
--
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