Error: could not find function "heatmap.2"
3
0
Entering edit mode
9.6 years ago
madkitty ▴ 690

I'm using DESeq2 and Bioconductor. When loading the heatmap I got the following error message :

Error: could not find function "heatmap.2"

Here is my pipeline:

> library( "genefilter" )

> topVarGenes <- head( order( rowVars( assay(rld) ), decreasing=TRUE ), 35 )

> heatmap.2( assay(rld)[ topVarGenes, ], scale="row",
+ trace="none", dendrogram="column",
+ col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255))
Error: could not find function "heatmap.2"

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252    LC_MONETARY=English_Canada.1252 LC_NUMERIC=C                   
[5] LC_TIME=English_Canada.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] genefilter_1.44.0       Biobase_2.22.0          DESeq2_1.2.10           RcppArmadillo_0.4.320.0 Rcpp_0.11.2             GenomicRanges_1.14.4   
[7] XVector_0.2.0           IRanges_1.20.7          BiocGenerics_0.8.0     

loaded via a namespace (and not attached):
 [1] annotate_1.40.1      AnnotationDbi_1.24.0 colorspace_1.2-4     DBI_0.2-7            digest_0.6.4         ggplot2_1.0.0       
 [7] grid_3.0.2           gtable_0.1.2         lattice_0.20-29      locfit_1.5-9.1       MASS_7.3-33          munsell_0.4.2       
[13] plyr_1.8.1           proto_0.3-10         RColorBrewer_1.0-5   reshape2_1.4         RSQLite_0.11.4       scales_0.2.4        
[19] splines_3.0.2        stats4_3.0.2         stringr_0.6.2        survival_2.37-7      XML_3.98-1.1         xtable_1.7-3        
deseq2 RNA-Seq heatmap • 29k views
ADD COMMENT
0
Entering edit mode

If you fail to find any function while using R just google it and see which package it comes from.

ADD REPLY
1
Entering edit mode

Sometimes you can even get their without bothering with a mouse. Though it seems this is not one of those times RSiteSearch("heatmap.2", restrict="functions") turns up another function but not the gplots on

ADD REPLY
2
Entering edit mode
9.6 years ago
madkitty ▴ 690

Just for those who are running into the same issue:

  1. Install the package gplots: install.packages("gplots")
  2. Run the library gplots: library(gplots)
ADD COMMENT
2
Entering edit mode
9.6 years ago

I believe this tutorial has instructions on how to install and use the heatmap functions (including heatmap.2):

http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/heatmap/

More specifically, you need to have the 'gplots' package installed.

ADD COMMENT
2
Entering edit mode
9.6 years ago
Assa Yeroslaviz ★ 1.8k

heatmap.2 needs the package gplots

ADD COMMENT

Login before adding your answer.

Traffic: 1694 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6