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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/seaborn commit 24dc6373560bd5e409fca84154634f5a528001c3
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">
2 <description>of all-vs-all column combinations</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6
7 <expand macro="edam"/>
8 <expand macro="requirements"/>
9 <expand macro="creator" />
10
11 <command detect_errors="exit_code"><![CDATA[
12 python3 '${run_script}'
13 ]]></command>
14
15 <configfiles>
16 <configfile name="run_script"><![CDATA[
17 index_col = $index_col
18
19 @INIT@
20
21 from scipy.stats import gaussian_kde
22
23 def scatter_density(x, y, **kwargs):
24 kwargs.pop('color')
25 # Calculate the point density
26 xy = np.vstack([x, y])
27 z = gaussian_kde(xy)(xy)
28 plt.scatter(x, y, c=z, cmap="jet", **kwargs)
29
30
31 g = sns.PairGrid(data)
32 g.map_lower(sns.regplot, scatter_kws=dict(s=4))
33 g.map_lower(sns.kdeplot, levels=4, color=".2")
34 g.map_upper(scatter_density, s=6)
35 g.map_diag(sns.histplot)
36
37 plt.savefig(f"{output_file}", format=output_format, dpi=300)
38 ]]></configfile>
39 </configfiles>
40 <inputs>
41 <expand macro="inputs"/>
42 <param argument="index_col" type="boolean" truevalue="0" falsevalue="None" checked="false" label="Is the first column the index?" help="Specify whether the first column of the input data should be treated as the index. If selected, the first column will not be used as data for plotting." />
43 <expand macro="transformation"/>
44 </inputs>
45 <outputs>
46 <data name="output_file" format="png" label="${tool.name} on ${on_string}" />
47 </outputs>
48 <tests>
49 <!-- Test 1: Generate a pairgrid plot with default settings -->
50 <test>
51 <param name="input_data" value="mtcars.txt" />
52 <output name="output_file">
53 <assert_contents>
54 <has_image_channels channels="4"/>
55 <has_image_height height="8250"/>
56 <has_image_width width="8250" />
57 <has_image_center_of_mass center_of_mass="4143.08, 4103.67" eps="0.1"/>
58 </assert_contents>
59 </output>
60 </test>
61 </tests>
62 <help><![CDATA[
63 .. class:: infomark
64
65 **What it does**
66
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.
68 The tool uses Seaborn's `PairGrid` functionality to create the matrix, with the following features:
69
70 - **Lower Triangle**: Regression plots and kernel density estimates (KDE).
71 - **Upper Triangle**: Scatterplots with point density coloring.
72 - **Diagonal**: Histograms of individual variables.
73
74 **Usage**
75
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.
77 2. **Advanced Options**: Apply transformations to the data (e.g., log10 or log2) before plotting.
78 3. **Output**: The tool generates a PNG image of the scatterplot matrix, which can be downloaded or used in further analyses.
79
80 **Input**
81
82 - **Input Data Table**: Upload your data file in TSV, CSV, TXT, or Parquet format. The file should contain numerical data for plotting.
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.
84 - **Data Transformation**: Apply transformations such as log10 or log2 to numerical data before plotting.
85
86 **Output**
87
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.
89
90 **Example Input**
91
92 Here is an example of a simple input dataset:
93
94 +------------+------------+------------+------------+
95 | Category | Value1 | Value2 | Value3 |
96 +============+============+============+============+
97 | A | 10 | 20 | 30 |
98 +------------+------------+------------+------------+
99 | B | 15 | 25 | 35 |
100 +------------+------------+------------+------------+
101 | C | 20 | 30 | 40 |
102 +------------+------------+------------+------------+
103
104 **Example Output**
105
106 The tool will generate a scatterplot matrix where:
107 - The lower triangle contains regression plots and KDE plots.
108 - The upper triangle contains scatterplots with point density coloring.
109 - The diagonal contains histograms of individual variables.
110
111 **Links**
112
113 - For more information about Seaborn's `PairGrid`, visit the official documentation: https://seaborn.pydata.org/generated/seaborn.PairGrid.html
114 - For detailed parameter descriptions, refer to the Galaxy tool documentation.
115 ]]></help>
116 <expand macro="citation"/>
117 </tool>