Plotting insert size vs base quality means

Question

[pablosolar.r]

Hi all!

I am using PySam to calculate the insert reads and the mean base quality for the reads of a BAM as follows:

import math
import pysam
import numpy as np
import matplotlib.pyplot as plt

bam_file = pysam.AlignmentFile("mybam.bam", "rb")

mean_base_qualities = []
insert_sizes = []
zipped = []
for read in bam_file:
    if read.is_paired and read.is_proper_pair:
        # length
        mean_bq = np.mean(read.query_qualities)
        read_length = read.query_alignment_length
        tlen = read.template_length
        insert_size = int(math.sqrt(math.pow(tlen, 2))-read_length)
        if insert_size > 0:
            zipped.append((mean_bq, insert_size))
            mean_base_qualities.append(mean_bq)
            insert_sizes.append(insert_size)


plt.plot(mean_base_qualities,insert_sizes)
plt.show()

Finally, I've got two huge lists representing the insert sizes and the mean base quality for a BAM reads, like:

insert_sizes = [291, 188, 165, 212, 186, 127, 240, 166, 120, 303, 255, ...

mean_base_qualities = [36.24324324324324, 34.73831775700935, 35.3448275862069, 30.64788732394366, 36.467289719626166, 22.673267326732674, 36.54216867469879, 31.20754716981132, 25.085714285714285, 34.65625,  ...

When I try to plot them I am getting the following graph but it is obviously wrong:

I also tried to sort the lists independently getting:

And also tried zipping the lists and different ways of plotting but with no succeed. Could you help me, please? What I am missing? Thank you in advance!

[h.mon]

I know next to nothing about matplotlib, but I think you want matplotlib.pyplot.scatter.