pheatmap: incomplete figure

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pheatmap: incomplete figure

R help mailing list-2
Dear R Community,
I tried to generate heatmap for a matrix of 1500 columns by 106 rows using the following R script:
> pheatmap(tf.vs.DE.1.removeAllZeroCol, fontsize=3,border_color=NA)
and got the graph (as attached Fig 1)

Since the column labels appear very crowded, I tried to increase the cellwidth to stretch the graph horizontally. The idea was to show the graph section by section, but with clear/readable column labels (not overlapped labels).
So I typed:
> pheatmap(tf.vs.DE.1.removeAllZeroCol, fontsize=3,cellwidth=3,cellheight=3,border_color=NA)
However, this time I only got middle part of the original heatmap (as attached Fig 2)
I wonder if there is way I could output the whole graph after such horizontal stretch. If not, how do I get the left end of the graph.
Thank you very much for any inputs!
Kind regards,
Ace
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example-graph.pdf (177K) Download Attachment
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Re: pheatmap: incomplete figure

David Winsemius

> On Sep 18, 2017, at 9:26 AM, Fix Ace via R-help <[hidden email]> wrote:
>
> Dear R Community,
> I tried to generate heatmap for a matrix of 1500 columns by 106 rows using the following R script:
>> pheatmap(tf.vs.DE.1.removeAllZeroCol, fontsize=3,border_color=NA)
> and got the graph (as attached Fig 1)
>
> Since the column labels appear very crowded, I tried to increase the cellwidth to stretch the graph horizontally. The idea was to show the graph section by section, but with clear/readable column labels (not overlapped labels).
> So I typed:
>> pheatmap(tf.vs.DE.1.removeAllZeroCol, fontsize=3,cellwidth=3,cellheight=3,border_color=NA)
> However, this time I only got middle part of the original heatmap (as attached Fig 2)
> I wonder if there is way I could output the whole graph after such horizontal stretch. If not, how do I get the left end of the graph.
>

Why not define a graphics device that is wider?

--

David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: pheatmap: incomplete figure

R help mailing list-2
Thank you so much for the reply! I thought the file would automatically adjust accordingly. But I just checked and found pheatmap does has width as parameter!
Ace

    On Monday, September 18, 2017 3:00 PM, David Winsemius <[hidden email]> wrote:
 

 

> On Sep 18, 2017, at 9:26 AM, Fix Ace via R-help <[hidden email]> wrote:
>
> Dear R Community,
> I tried to generate heatmap for a matrix of 1500 columns by 106 rows using the following R script:
>> pheatmap(tf.vs.DE.1.removeAllZeroCol, fontsize=3,border_color=NA)
> and got the graph (as attached Fig 1)
>
> Since the column labels appear very crowded, I tried to increase the cellwidth to stretch the graph horizontally. The idea was to show the graph section by section, but with clear/readable column labels (not overlapped labels).
> So I typed:
>> pheatmap(tf.vs.DE.1.removeAllZeroCol, fontsize=3,cellwidth=3,cellheight=3,border_color=NA)
> However, this time I only got middle part of the original heatmap (as attached Fig 2)
> I wonder if there is way I could output the whole graph after such horizontal stretch. If not, how do I get the left end of the graph.
>

Why not define a graphics device that is wider?

--

David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'  -Gehm's Corollary to Clarke's Third Law






   
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______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.