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correction of transformed sfs plot

master
tforest 2023-07-12 16:03:18 +02:00
parent a92dba2d25
commit f3fc152df3
1 changed files with 17 additions and 11 deletions
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28
sfs_tools.py
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@ -192,10 +192,10 @@ def sfs_from_parsed_vcf(n, vcf_dict, folded = True, diploid = True, phased = Fal
return SFS_values, count_pluriall
def barplot_sfs(sfs, xlab, ylab, folded=True, title = "Barplot", transformed = False):
def barplot_sfs(sfs, xlab, ylab, folded=True, title = "Barplot", transformed = False, normalized = False):
sfs_val = []
n = len(sfs.values())
print("n =", n)
sum_sites = sum(list(sfs.values()))
for k, ksi in sfs.items():
#ksi = list(sfs.values())[k-1]
# k+1 because k starts from 0
@ -209,24 +209,30 @@ 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(((k*(2*n - k)) / (2*n))*ksi)
val = ((k*(2*n - k)) / (2*n))*(ksi)
else:
sfs_val.append(ksi * k)
val = ksi * k
else:
sfs_val.append(ksi)
val = ksi
sfs_val.append(val)
#terminal case, same for folded or unfolded
if transformed:
sfs_val[-1] = list(sfs.values())[n-1] * n
last_bin = list(sfs.values())[n-1] * n/2
else:
sfs_val[-1] = list(sfs.values())[n-1]
last_bin = list(sfs.values())[n-1]
sfs_val[-1] = last_bin
if normalized:
ylab = "Fraction of SNPs"
sum_val = sum(sfs_val)
for k, sfs_bin in enumerate(sfs_val):
sfs_val[k] = sfs_bin / sum_val
#build the plot
title = title+" [folded="+str(folded)+"]"+" [transformed="+str(transformed)+"]"
title = title+" (n="+str(len(sfs_val)+1)+") [folded="+str(folded)+"]"+" [transformed="+str(transformed)+"]"
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)
print("Transformed SFS ( n =",len(sfs_val)+1, ") :", sfs_val)
customgraphics.barplot(x = [x for x in list(sfs.keys())], y= sfs_val, xlab = xlab, ylab = ylab, title = title)
plt.show()
if __name__ == "__main__":