Mercurial > repos > fubar > plotly_tabular_tool

annotate plotly_tabular_tool/README.md @ 3:51a0c2e0fbdf draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
1 # plotly_tabular_tool - plotly.express wrapped as a Galaxy tool.
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
2
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
3 ## Install to your Galaxy server from the toolshed - search for plotly_tabular_tool owned by fubar2
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
4
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
5 ### Example interactive plots and more at https://lazarus.name/demo/
0
7c166107a2e2 Uploaded
fubar
parents:
diff changeset
6
3
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
7 #### Non interactive screen grab of the tool output
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
8 ![Plotly blast html output screengrab](plotly_tabular_iris_sample.png)
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
9
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
10 Galaxy tool to create plotly interactive hover detail HTML plots from user selected columns of any Galaxy tabular data.
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
11 ## Recommended only for low dimensional data - a few thousand rows
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
12 Otherwise file sizes get huge and hover is useless to the viewer, so use non-interactive pdf for bigger data please.
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
13
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
14 ![Plotly tabular Galaxy tool form to generate the example](plotlytabular_toolform_sample.png)
0
7c166107a2e2 Uploaded
fubar
parents:
diff changeset
15
7c166107a2e2 Uploaded
fubar
parents:
diff changeset
16 Plotly.express makes a lot of clever design decisions.
3
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
17 Unfortunately, it gets totally confused with very small floats in scientific notation. Treats columns with 5.00e-204 as strings or something, so
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
18 strange and probably uninformative axes and plots will probably result if you try a blast evalue column without transformation.
0
7c166107a2e2 Uploaded
fubar
parents:
diff changeset
19 Note that all columns used for colour (legend) and the x/y axis tickmarks are truncated because they can squish up the plot.
3
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
20 *..* is appended at the truncation.
0
7c166107a2e2 Uploaded
fubar
parents:
diff changeset
21
1
449c918bc4cd Uploaded
fubar
parents: 0
diff changeset
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
449c918bc4cd Uploaded
fubar
parents: 0
diff changeset
23
3
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
24 ## Tool made with the Galaxy ToolFactory: https://github.com/fubar2/galaxy_tf_overlay
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
25 The current release includes this and a generic tabular version, and a java .jar wrapper in a history where the generating
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
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
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
27 made and the new tool generated without destroying the original sample.
1
449c918bc4cd Uploaded
fubar
parents: 0
diff changeset
28
3
51a0c2e0fbdf 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.
fubar
parents: 1
diff changeset
29