From efg at stowers-institute.org  Fri Feb 17 20:34:15 2006
From: efg at stowers-institute.org (Earl F. Glynn)
Date: Fri, 17 Feb 2006 13:34:15 -0600
Subject: [Rd] Could heatmap default to scale="none" ?
References: <adf71a630602161325p17a92220p4774012ac5e7a33d@mail.gmail.com>
Message-ID: <dt58fr$3fn$1@sea.gmane.org>

"Kevin Wright" <kwright68 at gmail.com> wrote in message
news:adf71a630602161325p17a92220p4774012ac5e7a33d at mail.gmail.com...
> (I have searched the email archives for discussions on this topic but
> have found nothing.)
> 1. Since the heatmap function is general-purpose (that is, not in a
> genomics package), wouldn't it be better to just use no scaling?
>
> 2. Why assume that the rows should be scaled instead of the columns?
> There appears to be an assumption on the structure of the data.  Is
> this assumption really warranted for a general-purpose function?
. . .
> The heatmap.2 function in the gplots package defaults to scale="none"
> and I argue that it would be better for the heatmap function to do the
> same.

I second this recommendation for exactly the same reasons.
Last week I spent an hour or so trying to figure out why the heatmap colors
for the same number were different across several related heatmaps. Turning
the scaling off removed the surprise color differences.  I will always want
scale="none" as my default and now must remember to always specify it.

If the default is not changed, I think a WARNING should be included in the
documentation about this.

efg



[Rd] Could heatmap default to scale="none" ?
Earl F. Glynn