Hi, there,
This is a simple question.
I'm trying to read my data from a .csv file and draw a heatmap with
heatmap.2.
Here is my code,
data=read.csv("file.csv", header=T)
x=as.matrix(data[,2:5])
heatmap.2(x)
The file.csv includes 5 columns and 118 rows. First columns are the
labels
for the each probe.
ID Temperature Agitation Oxygen Adhesion
BG03_B01 -0.098 0.013 0.007 0.064
BG04_A09 0.025 0.013 -0.011 -0.054
BG04_A11 -0.005 0.000 0.018 0.050
When I had my heatmap, the probes were labeled with the number from 1
to 117
instead of the ID numbers in the file. My question is how can I label
each
probe in the heatmap with their IDs. Thanks.
Wei
--
Wei Xu
Aquatic Animal Health Laboratory
Pathobiology and Diagnostic Investigation
College of Veterinary Medicine
Michigan State University
East Lansing, MI, 48824
Tel: 1-517-432-8258
[[alternative HTML version deleted]]
Hi Wei,
dat <- read.csv("file.csv", header = TRUE, row.names = 1)
heatmap.2(as.matrix(dat))
Best,
Jim
Wei Xu wrote:
> Hi, there,
>
> This is a simple question.
>
> I'm trying to read my data from a .csv file and draw a heatmap with
> heatmap.2.
> Here is my code,
>
> data=read.csv("file.csv", header=T)
> x=as.matrix(data[,2:5])
> heatmap.2(x)
>
> The file.csv includes 5 columns and 118 rows. First columns are the
labels
> for the each probe.
>
> ID Temperature Agitation Oxygen Adhesion
> BG03_B01 -0.098 0.013 0.007 0.064
> BG04_A09 0.025 0.013 -0.011 -0.054
> BG04_A11 -0.005 0.000 0.018 0.050
>
> When I had my heatmap, the probes were labeled with the number from
1 to 117
> instead of the ID numbers in the file. My question is how can I
label each
> probe in the heatmap with their IDs. Thanks.
>
> Wei
>
--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
Wei Xu wrote, On 16.03.2009 16:52:
> Hi, there,
>
> This is a simple question.
>
> I'm trying to read my data from a .csv file and draw a heatmap with
> heatmap.2.
> Here is my code,
>
> data=read.csv("file.csv", header=T)
> x=as.matrix(data[,2:5])
> heatmap.2(x)
>
> The file.csv includes 5 columns and 118 rows. First columns are the
labels
> for the each probe.
>
> ID Temperature Agitation Oxygen Adhesion
> BG03_B01 -0.098 0.013 0.007 0.064
> BG04_A09 0.025 0.013 -0.011 -0.054
> BG04_A11 -0.005 0.000 0.018 0.050
>
> When I had my heatmap, the probes were labeled with the number from
1 to 117
> instead of the ID numbers in the file. My question is how can I
label each
> probe in the heatmap with their IDs. Thanks.
>
> Wei
>
Try
heatmap.2(x, labRow=x$ID)
Christof
Hi Wei,
I think you need to set the row.names argument in read.csv to 1.
> ?read.csv
-----------------------
row.names: a vector of row names. This can be a vector giving the
actual row names, or a single number giving the column of
the
table which contains the row names, or character string
giving the name of the table column containing the row
names.
If there is a header and the first row contains one fewer
field than the number of columns, the first column in the
input is used for the row names. Otherwise if 'row.names'
is
missing, the rows are numbered.
Using 'row.names = NULL' forces row numbering. Missing or
'NULL' 'row.names' generate row names that are considered to
be 'automatic' (and not preserved by 'as.matrix').
-----------------------
Because the row.names are missing from your command, the rows were
numbered automatically (see above).
If you call:
> data=read.csv("file.csv", header=T, row.names=1)
it would automatically read the row labels which should show as
expected on the heatmap. I hope that solves this problem.
Best,
Saroj
----- Original Message -----
From: "Christof Winter" <winter@biotec.tu-dresden.de>
To: bioconductor at stat.math.ethz.ch
Cc: public-bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7 at
ciao.gmane.org
Sent: Monday, March 16, 2009 12:15:53 PM GMT -05:00 US/Canada Eastern
Subject: Re: [BioC] question about heatmap.2
Wei Xu wrote, On 16.03.2009 16:52:
> Hi, there,
>
> This is a simple question.
>
> I'm trying to read my data from a .csv file and draw a heatmap with
> heatmap.2.
> Here is my code,
>
> data=read.csv("file.csv", header=T)
> x=as.matrix(data[,2:5])
> heatmap.2(x)
>
> The file.csv includes 5 columns and 118 rows. First columns are the
labels
> for the each probe.
>
> ID Temperature Agitation Oxygen Adhesion
> BG03_B01 -0.098 0.013 0.007 0.064
> BG04_A09 0.025 0.013 -0.011 -0.054
> BG04_A11 -0.005 0.000 0.018 0.050
>
> When I had my heatmap, the probes were labeled with the number from
1 to 117
> instead of the ID numbers in the file. My question is how can I
label each
> probe in the heatmap with their IDs. Thanks.
>
> Wei
>
Try
heatmap.2(x, labRow=x$ID)
Christof
_______________________________________________
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Search the archives:
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--
Computational Biology
VBI @ Virginia Tech
Thanks a lot for the help. It works fine now.
Wei
On Mon, Mar 16, 2009 at 12:25 PM, Saroj K Mohapatra
<smohapat@vbi.vt.edu>wrote:
> Hi Wei,
>
> I think you need to set the row.names argument in read.csv to 1.
>
> > ?read.csv
> -----------------------
> row.names: a vector of row names. This can be a vector giving the
> actual row names, or a single number giving the column of
the
> table which contains the row names, or character string
> giving the name of the table column containing the row
names.
>
> If there is a header and the first row contains one fewer
> field than the number of columns, the first column in the
> input is used for the row names. Otherwise if 'row.names'
is
> missing, the rows are numbered.
>
> Using 'row.names = NULL' forces row numbering. Missing or
> 'NULL' 'row.names' generate row names that are considered
to
> be 'automatic' (and not preserved by 'as.matrix').
> -----------------------
>
> Because the row.names are missing from your command, the rows were
numbered
> automatically (see above).
>
> If you call:
> > data=read.csv("file.csv", header=T, row.names=1)
>
> it would automatically read the row labels which should show as
expected on
> the heatmap. I hope that solves this problem.
>
> Best,
> Saroj
>
> ----- Original Message -----
> From: "Christof Winter" <winter@biotec.tu-dresden.de>
> To: bioconductor@stat.math.ethz.ch
> Cc: public-
bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7@ciao.gmane.org
> Sent: Monday, March 16, 2009 12:15:53 PM GMT -05:00 US/Canada
Eastern
> Subject: Re: [BioC] question about heatmap.2
>
> Wei Xu wrote, On 16.03.2009 16:52:
> > Hi, there,
> >
> > This is a simple question.
> >
> > I'm trying to read my data from a .csv file and draw a heatmap
with
> > heatmap.2.
> > Here is my code,
> >
> > data=read.csv("file.csv", header=T)
> > x=as.matrix(data[,2:5])
> > heatmap.2(x)
> >
> > The file.csv includes 5 columns and 118 rows. First columns are
the
> labels
> > for the each probe.
> >
> > ID Temperature Agitation Oxygen Adhesion
> > BG03_B01 -0.098 0.013 0.007 0.064
> > BG04_A09 0.025 0.013 -0.011 -0.054
> > BG04_A11 -0.005 0.000 0.018 0.050
> >
> > When I had my heatmap, the probes were labeled with the number
from 1 to
> 117
> > instead of the ID numbers in the file. My question is how can I
label
> each
> > probe in the heatmap with their IDs. Thanks.
> >
> > Wei
> >
>
> Try
>
> heatmap.2(x, labRow=x$ID)
>
> Christof
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> --
> Computational Biology
> VBI @ Virginia Tech
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
--
Wei Xu
Aquatic Animal Health Laboratory
Pathobiology and Diagnostic Investigation
College of Veterinary Medicine
Michigan State University
East Lansing, MI, 48824
Tel: 1-517-432-8258
[[alternative HTML version deleted]]
Wei Xu wrote, On 16.03.2009 16:52:
> Hi, there,
>
> This is a simple question.
>
> I'm trying to read my data from a .csv file and draw a heatmap with
> heatmap.2.
> Here is my code,
>
> data=read.csv("file.csv", header=T)
> x=as.matrix(data[,2:5])
> heatmap.2(x)
>
> The file.csv includes 5 columns and 118 rows. First columns are the
labels
> for the each probe.
>
> ID Temperature Agitation Oxygen Adhesion
> BG03_B01 -0.098 0.013 0.007 0.064
> BG04_A09 0.025 0.013 -0.011 -0.054
> BG04_A11 -0.005 0.000 0.018 0.050
>
> When I had my heatmap, the probes were labeled with the number from
1 to 117
> instead of the ID numbers in the file. My question is how can I
label each
> probe in the heatmap with their IDs. Thanks.
>
> Wei
>
Try
heatmap.2(x, labRow=x$ID)
Christof
