Michael Young
2016-Sep-16 18:10 UTC
[R] Help modifying "aheatmap" or find a new heatmap package
I am currently using "aheatmap" which is generating heatmaps based on Pearson correlation. My data consists of RPKM values for genes from 2 groups. Each group has about 70 samples. Is there anyway that I can modify "aheatmap" so that it generates heat maps based on the actual input values (RPKM) and not Pearson correlation? I want the heatmap to show high heat for higher RPKM and cold heat for lower RPKM. If not, is there a package out there that can do this? Michael [[alternative HTML version deleted]]
Jim Lemon
2016-Sep-17 23:33 UTC
[R] Help modifying "aheatmap" or find a new heatmap package
Hi Michael, Maybe color2D.matplot (plotrix). Have a look at the examples. Jim On Sat, Sep 17, 2016 at 4:10 AM, Michael Young <mikeyoung83 at gmail.com> wrote:> I am currently using "aheatmap" which is generating heatmaps based on > Pearson correlation. My data consists of RPKM values for genes from 2 > groups. Each group has about 70 samples. > > Is there anyway that I can modify "aheatmap" so that it generates heat maps > based on the actual input values (RPKM) and not Pearson correlation? I > want the heatmap to show high heat for higher RPKM and cold heat for lower > RPKM. > If not, is there a package out there that can do this? > > Michael > > [[alternative HTML version deleted]] > > ______________________________________________ > 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.
Ulrik Stervbo
2016-Sep-18 05:22 UTC
[R] Help modifying "aheatmap" or find a new heatmap package
I am a huge fan of pheatmap and use it for all my heatmaps. Alternatively you can use ggplot2 and geom_tile Hth Ulrik Jim Lemon <drjimlemon at gmail.com> schrieb am So., 18. Sep. 2016 01:35:> Hi Michael, > Maybe color2D.matplot (plotrix). Have a look at the examples. > > Jim > > > On Sat, Sep 17, 2016 at 4:10 AM, Michael Young <mikeyoung83 at gmail.com> > wrote: > > I am currently using "aheatmap" which is generating heatmaps based on > > Pearson correlation. My data consists of RPKM values for genes from 2 > > groups. Each group has about 70 samples. > > > > Is there anyway that I can modify "aheatmap" so that it generates heat > maps > > based on the actual input values (RPKM) and not Pearson correlation? I > > want the heatmap to show high heat for higher RPKM and cold heat for > lower > > RPKM. > > If not, is there a package out there that can do this? > > > > Michael > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > 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. > > ______________________________________________ > 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. >[[alternative HTML version deleted]]