R help - Aug 2021 - collided row names in heatmap.2

Hi,

I am trying to draw a heatmap for my 45 topvar gene by the use of
heatmap.2, and when I set a srtRow=45 in my code(below):

heatmap.2( assay(rld)[ topVarGenes, ], srtRow=45,
scale="row",trace="none",
dendrogram="column",col = colorRampPalette( rev(brewer.pal(9,
"RdBu"))
)(255))

row names collided with each other in a messy way.

would you please help me to solve this problem? (also I'm a newbie beginner
using R Studio) Thank you so much
(also I attached the output image)

1. This is R-help. RStudio is a separate IDE from a private for-profit
company. You should go to their website for help with that:
https://www.rstudio.com/support/

2. I may be wrong, of course, but I believe your information is too
vague for folks to provide useful help: "row names collided with each
other in a messy way,' does not tell us much. What error message did
you get? Please provide a small, reproducible example (perhaps
via head(yourdatset, ...) see e.g. ?head and ?dput and
https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
. You may also wish to download and use the "reprex" package for this
purpose, instead. **See also the posting guide linked below.**

All of us were newbies at one time; take the time to learn these tools
and follow the advice for posting to R-help, and I believe that you
will have much greater success in getting useful help here as you
climb the learning curve.

Cheers,
Bert


Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Wed, Aug 11, 2021 at 9:07 AM Elham Hooshmand <e.hooshmand96 at
gmail.com> wrote:
>
> Hi,
>
> I am trying to draw a heatmap for my 45 topvar gene by the use of
> heatmap.2, and when I set a srtRow=45 in my code(below):
>
> heatmap.2( assay(rld)[ topVarGenes, ], srtRow=45,
scale="row",trace="none",
> dendrogram="column",col = colorRampPalette( rev(brewer.pal(9,
"RdBu"))
> )(255))
>
> row names collided with each other in a messy way.
>
> would you please help me to solve this problem? (also I'm a newbie
beginner
> using R Studio) Thank you so much
> (also I attached the output image)
> ______________________________________________
> 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.

Hi Elham,
Your image didn't get through, maybe PNG will work. Label crowding is
a common problem, whether horizontal or vertical. One solution is to
set a maximum length on label text (see truncString in the prettyR
package). Others are to stagger labels (staxlab in plotrix) or shift
them apart when crowded (spread.labels in plotrix). These functions
may not work with heatmap.2 (gplots). It will be easier to suggest
something if you can get your image through.

Jim

On Thu, Aug 12, 2021 at 2:07 AM Elham Hooshmand <e.hooshmand96 at
gmail.com> wrote:
>
> Hi,
>
> I am trying to draw a heatmap for my 45 topvar gene by the use of
> heatmap.2, and when I set a srtRow=45 in my code(below):
>
> heatmap.2( assay(rld)[ topVarGenes, ], srtRow=45,
scale="row",trace="none",
> dendrogram="column",col = colorRampPalette( rev(brewer.pal(9,
"RdBu"))
> )(255))
>
> row names collided with each other in a messy way.
>
> would you please help me to solve this problem? (also I'm a newbie
beginner
> using R Studio) Thank you so much
> (also I attached the output image)
> ______________________________________________
> 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.