Automatic and user-defined start position of heatmap indices (improve choice of "edges") #237

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joey711 opened this Issue Aug 15, 2013 · 2 comments

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joey711 commented Aug 15, 2013

include a user-definable option for the "start" sample and/or OTU, in case this helps better center the key clusters in the heatmap.

While the index ordering should continue to be done through a rational, reproducible, and well-defined method, the choice for "edges" of the heatmap are arbitrary, and can accidentally split clusters, which is itself misleading.

It is probably very helpful (and not terribly complicated) to provide the users with the option of giving an index for the OTU and sample index start positions, allowing them to iteratively select edge locations that better display the key clusters (avoid splitting).

There are also simple(-ish) ways to do this automatically that perhaps should be done by default, so that the truly obvious cases do not need any additional adjustment.

@ghost ghost assigned joey711 Aug 15, 2013

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joey711 commented Oct 28, 2013

This is implemented in a test-branch:

https://github.com/joey711/phyloseq/tree/heatmap-options

Running checks first before rolling into the master and closing this issue.

joey711 added a commit that referenced this issue Oct 30, 2013

1.7.6 new features for plot_heatmap() and improved import_mothur()
CHANGES IN VERSION 1.7.5
-------------------------

NEW FEATURES

	- User-specified axis ordering to plot_heatmap()

	- User-specified axis edges to plot_heatmap()

	- This addresses:
	  [Issue 237](#237)
	  [Issue 230](#230)

USER-VISIBLE CHANGES

	- New arguments to plot_heatmap():
	  `taxa.order`, `sample.order`, `first.sample`, `first.taxa`

CHANGES IN VERSION 1.7.4
-------------------------

NEW FEATURES

	- import_mothur now handles more formats

	- Added documentation to discourage .group/.list formats

joey711 added a commit that referenced this issue Oct 30, 2013

1.7.5 User-specified axis ordering and edges to plot_heatmap()
NEW FEATURES

	- User-specified axis ordering to plot_heatmap()

	- User-specified axis edges to plot_heatmap()

	- This addresses:
	  [Issue 237](#237)
	  [Issue 230](#230)
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joey711 commented Oct 30, 2013

I need to update the plot_heatmap tutorials to demonstrate the new options, but they are there now as of 1.7.5+

@joey711 joey711 closed this Oct 30, 2013

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