From 46ad7c44c821a62575dace80ba9e1b6b815d9b48 Mon Sep 17 00:00:00 2001
From: Veronique Legrand <vlegrand@pasteur.fr>
Date: Thu, 5 Dec 2024 15:52:45 +0100
Subject: [PATCH] changed the loading of data required to draw the global plot;
now read only 3 columns of the original hdf file.
---
jass/models/plots.py | 28 ++++++++++++++++------------
1 file changed, 16 insertions(+), 12 deletions(-)
diff --git a/jass/models/plots.py b/jass/models/plots.py
index f00b5ad6..ef60219e 100644
--- a/jass/models/plots.py
+++ b/jass/models/plots.py
@@ -17,10 +17,10 @@ from matplotlib import colors
import matplotlib.patches as mpatches
from scipy.stats import norm, chi2
import seaborn as sns
-import os
from pandas import DataFrame, read_hdf
import pandas as pd
+default_chunk_size=50
def replaceZeroes(df):
"""
@@ -32,30 +32,34 @@ def replaceZeroes(df):
df.values[df.values == 0] = min_nonzero
return df
-def create_global_plot(work_file_path: str, global_plot_path: str):
+
+def get_info_4_global_plot(work_file_path: str):
+ regions = read_hdf(work_file_path, "Regions",columns=['Region','CHR','MiddlePosition'])
+ print(regions.dtypes)
+ N_reg = regions.Region.max() # Keep biggest element in Region column
+ binf = regions.Region.iloc[0]
+ chr_considered = regions.CHR.unique()
+ length_chr = regions.groupby("CHR").MiddlePosition.max() / 10 ** 6
+ length_chr.loc[0] = 0
+ return N_reg,binf,chr_considered,length_chr
+
+def create_global_plot(work_file_path: str, global_plot_path: str, chunk_size:int =default_chunk_size):
"""
create_global_plot
generate genome-wide manhattan plot for a given set of phenotypes
"""
- regions = read_hdf(work_file_path, "Regions")
- #chr_length = regions.groupby('CHR').max().position
- N_reg= regions.Region.max()
+ N_reg,binf,chr_considered,length_chr=get_info_4_global_plot(work_file_path)
maxy = 0
fig = plt.figure(figsize=(30, 12))
ax = fig.add_subplot(111)
- chunk_size = 50
colors = [
'#4287f5',
'orangered'
]
- binf=regions.Region.iloc[0]
- bsup= binf+chunk_size
- chr_considered= regions.CHR.unique()
- length_chr = regions.groupby("CHR").MiddlePosition.max() / 10**6
- length_chr.loc[0] = 0
+
label = "Chr"+length_chr.loc[chr_considered].index.astype("str")
lab_pos = length_chr.loc[chr_considered]/2
@@ -63,7 +67,7 @@ def create_global_plot(work_file_path: str, global_plot_path: str):
pos_shift.index = pos_shift.index +1
pos_shift.loc[chr_considered[0]] = 0
lab_pos = lab_pos + [pos_shift.loc[i] for i in chr_considered]
-
+ bsup = binf + chunk_size
while binf < N_reg:
df = read_hdf(work_file_path, "SumStatTab", columns=["CHR","position", 'JASS_PVAL', "Region"], where = "Region >= {0} and Region < {1}".format(binf, bsup))
binf+= chunk_size
--
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