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annotate gaiac_violin_plot/gaiac_violin_plot.py @ 3:1f9e67edde6a draft default tip

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planemo upload for repository https://github.com/jaidevjoshi83/gaiac commit e9587f93346c7b55e1be00bad5844bf2db3ed03d-dirty
author jay
date Thu, 10 Jul 2025 19:42:02 +0000
parents 287d6cc86582
children
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
jay
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1 import numpy as np
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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2 import pandas as pd
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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3 import matplotlib.pyplot as plt
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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4 import seaborn as sns
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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5 #%matplotlib inline
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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6 import argparse as argparse
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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7 def violinplot(infile, clm_list_y, custom_xtick_labels, outfile, plottitle, fig_height, fig_width, clm_lab_y, clm_lab_x):
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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9 df=pd.read_csv(infile, sep="\t")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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11 cl = df.columns.tolist()
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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13 clms = [cl[int(x)-1] for x in clm_list_y.split(',')]
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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15 if custom_xtick_labels != None:
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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16 labels = custom_xtick_labels.split(',')
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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17 #print(labels)
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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18 else:
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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19 labels = clms
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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20 plt.figure(figsize=(int(fig_height),int(fig_width)))
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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21 sns.set(font_scale=0.8,style='whitegrid')
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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22 fig=sns.violinplot(data=df[clms])
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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23 fig.set_ylabel(clm_lab_y)
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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24 fig.set_xlabel(clm_lab_x)
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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25 fig.set_xticklabels(labels)
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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26 fig.set_title(plottitle)
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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27 plt.tight_layout
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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28 plt.savefig(outfile,dpi=300,bbox_inches="tight")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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31 if __name__=="__main__":
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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33 parser = argparse.ArgumentParser()
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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34 parser.add_argument("-I", "--infile", required=True, default=None, help="Input data file in TSV (tab-separated) format.")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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35 parser.add_argument("-C", "--column_list_y", required=False, default=False, help="Comma-separated list of column names to plot on the Y-axis.")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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36 parser.add_argument("-L", "--custom_xtick_name", required=False, default=None, help="Comma-separated list of custom legend names for the plot legend.")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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37 parser.add_argument("-O", "--output", required=False, default='Out.png', help="Filename for the output plot image (e.g. 'plot.png').")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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38 parser.add_argument("-T", "--title", required=False, default='Time Series plot', help="Title of the time series plot.")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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39 parser.add_argument("-H", "--height", required=False, default='14', help="Height of the figure in inches (default: 14).")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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40 parser.add_argument("-W", "--width", required=False, default='12', help="Width of the figure in inches (default: 12).")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
jay
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41 parser.add_argument("-Y", "--ylab", required=False, default='Y label', help="Label for the Y-axis (default: 'Y label').")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
jay
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42 parser.add_argument("-X", "--xlab", required=False, default='X label(time)', help="Label for the X-axis (default: 'X label(time)').")
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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44 args = parser.parse_args()
287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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287d6cc86582 planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
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46 violinplot(args.infile, args.column_list_y, args.custom_xtick_name, args.output, args.title, args.width, args.height, args.ylab, args.xlab)