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Updated with latest ToolFactory with change_format for outputs so can make a png or html and it has an informative label since on $foo can be used.
author fubar
date Fri, 04 Aug 2023 02:00:28 +0000
parents 449c918bc4cd
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2:08cc7a481af8 3:51a0c2e0fbdf
1 # plotly_tabular_tool 1 # plotly_tabular_tool - plotly.express wrapped as a Galaxy tool.
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3 Galaxy tool to create plotly plots from user selected columns of any Galaxy tabular data. 3 ## Install to your Galaxy server from the toolshed - search for plotly_tabular_tool owned by fubar2
4 Example interactive plots at https://lazarus.name/demo/ 4
5 ### Example interactive plots and more at https://lazarus.name/demo/
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7 #### Non interactive screen grab of the tool output
8 ![Plotly blast html output screengrab](plotly_tabular_iris_sample.png)
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10 Galaxy tool to create plotly interactive hover detail HTML plots from user selected columns of any Galaxy tabular data.
11 ## Recommended only for low dimensional data - a few thousand rows
12 Otherwise file sizes get huge and hover is useless to the viewer, so use non-interactive pdf for bigger data please.
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14 ![Plotly tabular Galaxy tool form to generate the example](plotlytabular_toolform_sample.png)
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6 Plotly.express makes a lot of clever design decisions. 16 Plotly.express makes a lot of clever design decisions.
7 Unfortunately, it gets totally confused with evalue columns because it thinks scientific notation like 5.00e-204 is a string or something. 17 Unfortunately, it gets totally confused with very small floats in scientific notation. Treats columns with 5.00e-204 as strings or something, so
8 Strange and probably uninformative axes and plots will probably result if you try a blast evalue column without transformation. 18 strange and probably uninformative axes and plots will probably result if you try a blast evalue column without transformation.
9 Note that all columns used for colour (legend) and the x/y axis tickmarks are truncated because they can squish up the plot. 19 Note that all columns used for colour (legend) and the x/y axis tickmarks are truncated because they can squish up the plot.
10 .. is added at the end to show truncation. 20 *..* is appended at the truncation.
11 21
12 A specialised version for 25 column Galaxy blastn search outputs is also available. It uses this code mostly, but adds a default header and auto-transformation of the evalue column -log10(x) to make them more like the bitscore 22 A specialised version for 25 column Galaxy blastn search outputs is also available. It uses this code mostly, but adds a default header and auto-transformation of the evalue column -log10(x) to make them more like the bitscore
13 23
24 ## Tool made with the Galaxy ToolFactory: https://github.com/fubar2/galaxy_tf_overlay
25 The current release includes this and a generic tabular version, and a java .jar wrapper in a history where the generating
26 ToolFactory form can be recreated using the redo button. Editing the tool id will make a new tool, so all other edits to parameters can be
27 made and the new tool generated without destroying the original sample.
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