Add news item about KM/C-PH survival analysis tool using the lifelines package

content/news/2023-08-07-generic-tabular-plotter/index.md

@@ -40,14 +40,16 @@ This Iris test data is relatively tiny with about 150 rows, so the points
 are nicely separated, making the hover information easy to use.
 
 Interactive html plots work best for at most, a few thousand well spread points,
-so the hover display is easy to control.
+so the hover display is easy to control. They reliably freeze up using a recent firefox build if 10k rows, so this tool
+now always fails if >5k rows are chosen for html output. Advice to this effect has been
+added to the form.
 
-Interactive html output is available in stand alone format, where 3MB of javascript is included,
+For <5k rows of data, interactive html output is available in stand alone format, where 3MB of javascript is included,
 allowing it to be viewed offline. Short form html requires an internet connection to download the
 javascript into the browser so cannot be viewed offline.
 
-PNG plots are recommended for large numbers of rows, since the the hover function tends to be less useful
-when the plot is very crowded.
+Only PNG output options will work for large numbers of rows, since the the hover function tends to be less useful
+when the plot is very crowded, and large html outputs can make browser windows freeze up.
 
 If the tabular data does not have a header row of column names, the user can supply and use a
 comma delimited list, as the "header" parameter on the tool form.

content/news/2023-08-11-lifelineskmcph/index.md

@@ -0,0 +1,74 @@
+---
+title: "Survival analysis for right censored data using lifelines"
+date: "2023-08-11"
+authors: Ross Lazarus
+authors_structured:
+- github: fubar2
+tease: "Kaplan-Meier and Cox proportional hazards models are available for testing in Galaxy"
+hide_tease: true
+subsites: [all]
+---
+
+A tool that wraps the [lifelines](https://lifelines.readthedocs.io/en/latest/Survival%20Analysis%20intro.html) package is available
+
+Any Galaxy tabular data with a column containing time and status in a format suitable for pandas and lifelines can be used as input.
+Time might be an integer month since a treatment. Status might be 0 for no failure at observation time, 1 for death or failure.
+Other columns can be used as groups for KM, or as covariates for Cox-PH.
+
+If the data has no header row, the default column names are col1,....coln unless a header parameter, containing column names in order
+delimited with "," is supplied on the tool form.
+Whatever the source of column names, they must match the ones provided as parameters.
+
+### Demonstration with the Rossi recidivism data from lifelines tutorials
+
+Runs Kaplan-Meier and generates a plot. Optional grouping variable.
+
+Plots show confidence intervals
+
+![KM plot sample](lifelines_rossi_km.png)
+
+If 2 groups, runs a log-rank test for difference.
+
+![KM plot sample](lifelines_report.png)
+
+If a comma separated list (for example: prio, age, race, mar, fin) of covariate column names is provided,
+a Cox proportional hazards model is run, the assumption of proportionality is tested, and
+recommendations made.
+
+![KM plot sample](lifelines_rossi_schoenfeld.png)
+
+Also included are partial plots for each covariate like these from the Rossi recidivism lifelines sample data
+used in the tool test.
+
+![C-PH partial plot samples](agepartialrossi.png)
+
+![C-PH partial plot samples](parolepartialrossi.png)
+
+Uses pandas read_csv with tabular delimiters so should work with any tabular data with the required columns - time and status for observations.
+
+Issues to https://github.com/fubar2/lifelines_tool please.
+Autogenerated so pull requests are possibly meaningless but regeneration of a new version should work.
+
+### Installation for testing
+
+The [lifelines tool](https://toolshed.g2.bx.psu.edu/view/fubar/lifelines_km_cph_tool/dd5e65893cb8), owned by fubar, is available for testing, in the main Galaxy Toolshed.
+It is very new and so not suitable for production use yet. Please let me know if it works for you.
+
+### Tool code
+
+The tool code is available for review at the <a href="https://github.com/fubar2/lifelines_tool">github repository</a> where issues should
+be raised when there are problems or suggestions. This is machine generated code, so pull requests don't
+make much sense. The generator can be rerun with simple changes easily so please suggest
+any useful things you'd like to see.
+
+
+### Tool made with the [Galaxy ToolFactory](https://github.com/fubar2/galaxy_tf_overlay)
+
+Galaxy Training Network tutorials [ are available here](https://training.galaxyproject.org/training-material/topics/dev/tutorials/tool-generators/tutorial.html)
+
+The github repository contains a Galaxy history that was exported after generating the current version of the tool.
+If that history is imported into a ToolFactory instance, the generating ToolFactory form can be recreated
+using the redo button. Editing the tool id will make a new tool, so edits to parameters can be made and the
+new tool generated and tested.
+
+