Mercurial > repos > iuc > seaborn_pairgrid

annotate seaborn_pairgrid.xml @ 0:4a46d83cb08f draft default tip

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author iuc
date Wed, 14 May 2025 08:39:22 +0000
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1 <tool id="seaborn_pairgrid" name="seaborn pair-wise scatterplot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0" license="MIT">
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2 <description>of all-vs-all column combinations</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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7 <expand macro="edam"/>
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8 <expand macro="requirements"/>
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9 <expand macro="creator" />
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11 <command detect_errors="exit_code"><![CDATA[
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12 python3 '${run_script}'
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13 ]]></command>
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15 <configfiles>
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16 <configfile name="run_script"><![CDATA[
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17 index_col = $index_col
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19 @INIT@
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21 from scipy.stats import gaussian_kde
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23 def scatter_density(x, y, **kwargs):
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24 kwargs.pop('color')
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25 # Calculate the point density
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26 xy = np.vstack([x, y])
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27 z = gaussian_kde(xy)(xy)
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28 plt.scatter(x, y, c=z, cmap="jet", **kwargs)
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31 g = sns.PairGrid(data)
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32 g.map_lower(sns.regplot, scatter_kws=dict(s=4))
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33 g.map_lower(sns.kdeplot, levels=4, color=".2")
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34 g.map_upper(scatter_density, s=6)
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35 g.map_diag(sns.histplot)
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36
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37 plt.savefig(f"{output_file}", format=output_format, dpi=300)
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38 ]]></configfile>
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39 </configfiles>
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40 <inputs>
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41 <expand macro="inputs"/>
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42 <param argument="index_col" type="boolean" truevalue="0" falsevalue="None" checked="false" label="Is the first column the index?" help="Specify whether the first column of the input data should be treated as the index. If selected, the first column will not be used as data for plotting." />
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43 <expand macro="transformation"/>
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44 </inputs>
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45 <outputs>
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46 <data name="output_file" format="png" label="${tool.name} on ${on_string}" />
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47 </outputs>
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48 <tests>
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49 <!-- Test 1: Generate a pairgrid plot with default settings -->
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50 <test>
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51 <param name="input_data" value="mtcars.txt" />
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52 <output name="output_file">
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53 <assert_contents>
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54 <has_image_channels channels="4"/>
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55 <has_image_height height="8250"/>
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56 <has_image_width width="8250" />
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57 <has_image_center_of_mass center_of_mass="4143.08, 4103.67" eps="0.1"/>
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58 </assert_contents>
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59 </output>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 .. class:: infomark
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64
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65 **What it does**
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66
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67 This tool generates a scatterplot matrix (pair-wise scatterplots) of all column combinations in the input dataset using the Seaborn library. The scatterplot matrix provides a visual summary of the relationships between variables in the dataset, making it useful for exploratory data analysis.
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68 The tool uses Seaborn's `PairGrid` functionality to create the matrix, with the following features:
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69
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70 - **Lower Triangle**: Regression plots and kernel density estimates (KDE).
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71 - **Upper Triangle**: Scatterplots with point density coloring.
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72 - **Diagonal**: Histograms of individual variables.
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73
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74 **Usage**
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75
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76 1. **Input**: Provide a tabular data file in one of the supported formats (TSV, CSV, TXT, or Parquet). Optionally, specify whether the first column should be treated as the index.
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77 2. **Advanced Options**: Apply transformations to the data (e.g., log10 or log2) before plotting.
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78 3. **Output**: The tool generates a PNG image of the scatterplot matrix, which can be downloaded or used in further analyses.
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79
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80 **Input**
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81
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82 - **Input Data Table**: Upload your data file in TSV, CSV, TXT, or Parquet format. The file should contain numerical data for plotting.
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83 - **Index Column**: Specify whether the first column of the input data should be treated as the index. If selected, the first column will not be used for plotting.
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84 - **Data Transformation**: Apply transformations such as log10 or log2 to numerical data before plotting.
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85
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86 **Output**
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87
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88 The tool generates a PNG file containing the scatterplot matrix. The file can be downloaded or used as input for other tools in Galaxy.
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89
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90 **Example Input**
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91
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92 Here is an example of a simple input dataset:
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93
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94 +------------+------------+------------+------------+
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95 | Category | Value1 | Value2 | Value3 |
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96 +============+============+============+============+
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97 | A | 10 | 20 | 30 |
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98 +------------+------------+------------+------------+
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99 | B | 15 | 25 | 35 |
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100 +------------+------------+------------+------------+
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101 | C | 20 | 30 | 40 |
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102 +------------+------------+------------+------------+
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103
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104 **Example Output**
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105
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106 The tool will generate a scatterplot matrix where:
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107 - The lower triangle contains regression plots and KDE plots.
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108 - The upper triangle contains scatterplots with point density coloring.
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109 - The diagonal contains histograms of individual variables.
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110
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111 **Links**
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112
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113 - For more information about Seaborn's `PairGrid`, visit the official documentation: https://seaborn.pydata.org/generated/seaborn.PairGrid.html
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114 - For detailed parameter descriptions, refer to the Galaxy tool documentation.
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115 ]]></help>
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116 <expand macro="citation"/>
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117 </tool>