Mercurial > repos > fubar > plotly_tabular_tool
diff plotly_tabular_tool/README.md @ 3:51a0c2e0fbdf draft
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 |
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date | Fri, 04 Aug 2023 02:00:28 +0000 |
parents | 449c918bc4cd |
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--- a/plotly_tabular_tool/README.md Fri Jul 28 06:01:53 2023 +0000 +++ b/plotly_tabular_tool/README.md Fri Aug 04 02:00:28 2023 +0000 @@ -1,14 +1,29 @@ -# plotly_tabular_tool +# plotly_tabular_tool - plotly.express wrapped as a Galaxy tool. + +## Install to your Galaxy server from the toolshed - search for plotly_tabular_tool owned by fubar2 + +### Example interactive plots and more at https://lazarus.name/demo/ -Galaxy tool to create plotly plots from user selected columns of any Galaxy tabular data. -Example interactive plots at https://lazarus.name/demo/ +#### Non interactive screen grab of the tool output +![Plotly blast html output screengrab](plotly_tabular_iris_sample.png) + +Galaxy tool to create plotly interactive hover detail HTML plots from user selected columns of any Galaxy tabular data. +## Recommended only for low dimensional data - a few thousand rows +Otherwise file sizes get huge and hover is useless to the viewer, so use non-interactive pdf for bigger data please. + +![Plotly tabular Galaxy tool form to generate the example](plotlytabular_toolform_sample.png) Plotly.express makes a lot of clever design decisions. -Unfortunately, it gets totally confused with evalue columns because it thinks scientific notation like 5.00e-204 is a string or something. -Strange and probably uninformative axes and plots will probably result if you try a blast evalue column without transformation. +Unfortunately, it gets totally confused with very small floats in scientific notation. Treats columns with 5.00e-204 as strings or something, so +strange and probably uninformative axes and plots will probably result if you try a blast evalue column without transformation. Note that all columns used for colour (legend) and the x/y axis tickmarks are truncated because they can squish up the plot. -.. is added at the end to show truncation. +*..* is appended at the truncation. 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 +## Tool made with the Galaxy ToolFactory: https://github.com/fubar2/galaxy_tf_overlay +The current release includes this and a generic tabular version, and a java .jar wrapper in a history where the generating +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 +made and the new tool generated without destroying the original sample. +