R help - Oct 2016 - Please help with creating the improved image with pheatmap package

Hi all,

I'm trying to show about 190 items using "pheatmap" package.
I'm working
with R 3.3.1 on windows 7. I used the following code:

pheatmap(mat_data, cellwidth=20, cluster_rows = FALSE, cluster_cols FALSE,
fontsize=5, fontsize_row=5, margins=c(5,10))


The resulted image is attached. Please take a look at it. As you could see,
the image quality is not good, in fact, the label of each row has not been
appropriately shown at all in the picture. Could you please help me how I
can modify the code to improve the image?




Thank you very much in advance

Best regards,
Maryam
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> On Oct 3, 2016, at 4:43 AM, maryam moazam <setareh227 at gmail.com>
wrote:
> 
> Hi all,
> 
> I'm trying to show about 190 items using "pheatmap" package.
I'm working
> with R 3.3.1 on windows 7. I used the following code:
> 
> pheatmap(mat_data, cellwidth=20, cluster_rows = FALSE, cluster_cols >
FALSE, fontsize=5, fontsize_row=5, margins=c(5,10))
> 
> 
> The resulted image is attached. Please take a look at it. As you could see,
> the image quality is not good, in fact, the label of each row has not been
> appropriately shown at all in the picture. Could you please help me how I
> can modify the code to improve the image?
> 
If png() is your desired target then you probably will want to set different
plotting parameters since your image is so tall.

?grDevices
?png   # guessing you need to set 'height' much higher
?par
?points  # good examples of low-level control 

> 
> 
> 
> Thank you very much in advance
> 
> Best regards,
> Maryam
> <image_pheatmap.png>______________________________________________
> R-help at r-project.org 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.
David Winsemius
Alameda, CA, USA

Hi Maryam,
Your labels have been "greeked" as the font is too small to be
displayed properly. If you must use PNG format, specify your image
file at least twice as high.

png("pheatmap.png",width=1254,height=5000)

PDF would be a better choice as you can just zoom in and scroll down.

Jim


On Mon, Oct 3, 2016 at 10:43 PM, maryam moazam <setareh227 at gmail.com>
wrote:
> Hi all,
>
> I'm trying to show about 190 items using "pheatmap" package.
I'm working
> with R 3.3.1 on windows 7. I used the following code:
>
> pheatmap(mat_data, cellwidth=20, cluster_rows = FALSE, cluster_cols >
FALSE, fontsize=5, fontsize_row=5, margins=c(5,10))
>
>
> The resulted image is attached. Please take a look at it. As you could see,
> the image quality is not good, in fact, the label of each row has not been
> appropriately shown at all in the picture. Could you please help me how I
> can modify the code to improve the image?
>
>
>
>
> Thank you very much in advance
>
> Best regards,
> Maryam
>
> ______________________________________________
> R-help at r-project.org 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.