R help - Aug 2011 - heatmap is producing unwanted horizontal and vertical lines?

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.
	[[alternative HTML version deleted]]

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. 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?

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: ? ? ?
?Colin Ford <col_ford at yahoo.com> 
To: ? ? ?
?"r-help at r-project.org"
<r-help at r-project.org> 
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.
? ? ? ? ? ? ? ?
[[alternative HTML version deleted]]

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