png files with additional tick labels
warthmann opened this issue · 4 comments
Hello,
I have installed samplot through conda. During some plots I am getting a warning, ie.
/samplot.py:3014: UserWarning: set_ticklabels() should only be used with a fixed number of ticks, i.e. after set_ticks() or using a FixedLocator.
curr_ax.set_xticklabels(labels, fontsize=xaxis_label_fontsize)
and also I do have additional tick marks in my pngs. It concerns all plots. An example is attached. Help in removing those tick marks is apppreciated
thanks a lot
best
Norman
Could you please try running the develop version of samplot. You can install this using e.g.
pip install git+https://github.com/ryanlayer/samplot.git
There has been a lot of changes since the latest conda version so please test this and see if the problems still appear.
I was just about to open this issue - I am running the develop version, (or v1.3.1 at any rate) - originally installed via conda, upgraded via the above pip command.
Command
time python -m samplot plot -n "PromethION NA12878" "PromethION NB4" "Promethion 22Rv1" -b all_barcode05.sequenc
ed.fastq.bam all_barcode06.sequenced.fastq.bam all_barcode06.sequenced.fastq.bam -o figure_4_prom.png -c chr17 -s 40245924 -e 40445924 -c chr15 -s 73934033 -e 74134033 -t BND
/home/prom/miniforge3/envs/samplot/lib/python3.10/site-packages/samplot/samplot.py:2911: UserWarning: set_ticklabels() should only be used with a fixed number of ticks, i.e. after set_ti
cks() or using a FixedLocator.
curr_ax.set_xticklabels(labels, fontsize=xaxis_label_fontsize)
real 0m16.659s
user 0m20.635s
sys 0m6.787s
Version
python -m samplot --version
samplot 1.3.1
Plot produced
OS - Ubuntu 20.04 LTS
Installed packages
pip list
Package Version
--------------- -------
contourpy 1.0.5
cycler 0.11.0
fonttools 4.25.0
Jinja2 3.1.2
kiwisolver 1.4.4
MarkupSafe 2.1.1
matplotlib 3.8.0
numpy 1.26.0
packaging 23.1
Pillow 10.0.1
pip 23.3
pyparsing 3.0.9
pysam 0.22.0
python-dateutil 2.8.2
samplot 1.3.1
setuptools 68.0.0
six 1.16.0
wget 3.2
wheel 0.41.2Downgrading matplotlib fixes this issue - I chose 3.6.0 at random, and the ticks were fixed
I can confirm that the problem goes away when downgrading matplotlib. Note that also the borders (black lines) around the plot go away.
$pip list
$conda list
$pip uninstall matplotlib
$pip install --force-reinstall matplotlib==3.6.0