[R] heatmap is producing unwanted horizontal and vertical lines?

[David Winsemius]

On Aug 8, 2011, at 11:53 AM, Colin Ford wrote:

> Hi Pete,
>
> I thought it might be something to do with NA's when I first started  
> but its not. I've attached both the image output and the data.

No, you haven't. Probably was an unacceptable file type.

> Its almost as if the blocks in the heatmap are not quite meshing  
> together? I've tried heatmap.2 as well and that gave the same  
> result. I also just tried the image command and that was giving the  
> same result as well.
>
> What I'm wanting are blocks together without the white lines going  
> through but just cant seem to find a way to do that?

Sounds like the old problem of buggy pdf viewers relating to problems  
with anti-aliasing. Further commentary would probably be available had  
you included any machine or OS specifics,  but why not search in the  
Archives before sending further material?

Search terms likely to be productive: white lines anti-aliasing pdf

(or variations there within)

-- 
David


>
> Best regards,
> Col.
>
> ________________________________
> From: Peter Morgan <MorganPH at cardiff.ac.uk>
> To: Colin Ford <col_ford at yahoo.com>
> Sent: Monday, 8 August 2011, 14:37
> Subject: Re: [R] heatmap is producing unwanted horizontal and  
> vertical lines?
>
>
> Hi Col,
>
> Without seeing your data and the heatmap
> you are plotting it is hard to tell what is going on. Are the NAs in  
> any
> pattern?  NAs appear in heatmap as the background colour which is
> white by default since they are plotted transparently (see the  
> image( )
> command for details). If this is the case, you could be seeing the  
> pattern
> of NAs plotted in white.
>
> Also, have you tried the the heatmap.2(
> ) option in gplots?
>
> Regards,
>
> Pete
> From:

> Date:
>  08/08/2011 13:05
> Subject:
>    [R] heatmap
> is producing unwanted horizontal and vertical lines?
> Sent by:
>    r-help-bounces at r-project.org
> ________________________________
>
> Hello,
>
> I must start by saying that I am an R novice and am sorry if this is a
> no-brainer...
>
> I have an csv file that contains a grid of 300x300 data points. Each  
> point
> represents a 1Km square on a map. Each point is either a floating  
> point number or NA. I load the
> data in with:
>
>   data <- read.csv("matrix.csv", sep=',')
>
> Convert the data to a matrix with:
>
>   data_matrix <- data.matrix(data)
>
> and then produce the heatmap with:
>
>   data_heatmap <-  
> heatmap(data_matrix,Rowv=NA,Colv='Rowv',margin=c(0,0))
>
> The heatmap is displayed in a separate window as expected and
> looks correct apart  from fine white banding lines spaced out evenly  
> over the image running horizontally across the image?
>
> At first I thought it was my data but I checked that and its not. If I
> resize the image I then see white vertical lines and different  
> horizontal
> lines appear?
>
> I've tried a number of different settings but can't seem to get
> rid of these lines.
> If I can get rid of them the image will be ideal and just what I want.
> Does anyone have any idea of what I'm doing wrong?
>
> Best regards,
> Col.

-- 
David Winsemius, MD
West Hartford, CT