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correction for sfs transform plot

master
tforest 2022-07-08 14:15:41 +02:00
parent a8b5c1aa6f
commit a92dba2d25
2 changed files with 15 additions and 11 deletions
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3
customgraphics.py
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@ -202,10 +202,13 @@ def scatter(x, y, ylab=None, xlab=None, title=None):
def barplot(x=None, y=None, ylab=None, xlab=None, title=None):
if x:
x = list(x)
plt.xticks(x)
plt.bar(x, y)
else:
x = list(range(len(y)))
plt.bar(x, y)
plt.xticks(x)
if ylab:
plt.ylabel(ylab)
if xlab:

23
sfs_tools.py
View File

@ -20,6 +20,7 @@ Rectify SFS comp in parsed funct.
import gzip
import sys
import matplotlib.pyplot as plt
from frst import customgraphics
def sfs_from_vcf(n, vcf_file, folded = True, diploid = True, phased = False, verbose = False,
strip = False, count_ext = False):
@ -194,8 +195,9 @@ def sfs_from_parsed_vcf(n, vcf_dict, folded = True, diploid = True, phased = Fal
def barplot_sfs(sfs, xlab, ylab, folded=True, title = "Barplot", transformed = False):
sfs_val = []
n = len(sfs.values())
for k in range(1, n):
ksi = list(sfs.values())[k-1]
print("n =", n)
for k, ksi in sfs.items():
#ksi = list(sfs.values())[k-1]
# k+1 because k starts from 0
# if folded:
# # ?check if 2*n or not?
@ -207,7 +209,8 @@ def barplot_sfs(sfs, xlab, ylab, folded=True, title = "Barplot", transformed =
# sfs_val.append(ksi)
if transformed:
if folded:
sfs_val.append(ksi * k * (2*n - k))
#sfs_val.append(ksi * k * (2*n - k))
sfs_val.append(((k*(2*n - k)) / (2*n))*ksi)
else:
sfs_val.append(ksi * k)
else:
@ -215,17 +218,15 @@ def barplot_sfs(sfs, xlab, ylab, folded=True, title = "Barplot", transformed =
#terminal case, same for folded or unfolded
if transformed:
sfs_val.append(list(sfs.values())[n-1] * n)
sfs_val[-1] = list(sfs.values())[n-1] * n
else:
sfs_val.append(list(sfs.values())[n-1])
sfs_val[-1] = list(sfs.values())[n-1]
#build the plot
title = title+" [folded="+str(folded)+"]"+" [transformed="+str(transformed)+"]"
if ylab:
plt.ylabel(ylab)
if xlab:
plt.xlabel(xlab)
plt.title(title)
plt.bar([i+1 for i in sfs.keys()], sfs_val)
print("SFS =", sfs)
if transformed:
print("Transformed SFS ( n =",len(sfs_val), ") :", sfs_val)
customgraphics.barplot(x = sfs.keys(), y= sfs_val, xlab = xlab, ylab = ylab, title = title)
plt.show()
if __name__ == "__main__":