Hi,

If I try to plot annHeatmap with  my data or the example, I have an error.

Can you tell me which mistake I made and what I need to correct to use it ?

Regards,

Tiphaine

require(Biobase)
data(sample.ExpressionSet)
ex1 = sample.ExpressionSet[51:85,]
map1 = annHeatmap2(exprs(ex1), ann=list(Col=list(data=pData(ex1))),
                   cluster=list(Col=list(cuth=3000)))
plot(map1)

The error is :

Error in plot.default(xlim, ylim, xlim = xlim, ylim = ylim, type = "n",  :
  formal argument "type" matched by multiple actual arguments
In addition: Warning message:
In rep(cellres, length = 2) : 'x' is NULL so the result will be NULL

sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] RColorBrewer_1.1-2   vegan_2.2-1          lattice_0.20-29      permute_0.8-3       
 [5] Heatplus_2.12.0      BiocInstaller_1.16.1 knitr_1.9            psych_1.5.1         
 [9] DiffCorr_0.2         fdrtool_1.2.13       igraph_0.7.1         pcaMethods_1.56.0   
[13] Biobase_2.26.0       BiocGenerics_0.12.1  qgraph_1.3           seriation_1.0-14    
[17] plotrix_3.5-11       pbkrtest_0.4-2       influence.ME_0.9-5   lme4_1.1-7          
[21] Rcpp_0.11.4          Matrix_1.1-5         swamp_1.2.3          MASS_7.3-35         
[25] amap_0.8-14          impute_1.40.0        plyr_1.8.1           ggplot2_1.0.0       
[29] gplots_2.16.0        ade4_1.6-2          

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3     bitops_1.0-6        caTools_1.17.1      cluster_2.0.1      
 [5] colorspace_1.2-4    corpcor_1.6.7       d3Network_0.5.2.1   digest_0.6.8       
 [9] ellipse_0.3-8       evaluate_0.5.5      foreign_0.8-62      formatR_1.0        
[13] Formula_1.2-0       gclus_1.3.1         gdata_2.13.3        ggm_2.3            
[17] glasso_1.8          grid_3.1.2          gtable_0.1.2        gtools_3.4.1       
[21] Hmisc_3.14-6        huge_1.2.6          jpeg_0.1-8          KernSmooth_2.23-13
[25] latticeExtra_0.6-26 lavaan_0.5-17       matrixcalc_1.0-3    mgcv_1.8-4         
[29] minqa_1.2.4         mnormt_1.5-1        munsell_0.4.2       nlme_3.1-119       
[33] nloptr_1.0.4        nnet_7.3-9          pbivnorm_0.6.0      pixmap_0.4-11      
[37] png_0.1-7           proto_0.3-10        quadprog_1.5-5      reshape2_1.4.1     
[41] rjson_0.2.15        rpart_4.1-8         rtiff_1.4.4         scales_0.2.4       
[45] sem_3.1-5           sendplot_4.0.0      sna_2.3-2           splines_3.1.2      
[49] stats4_3.1.2        stringr_0.6.2       survival_2.37-7     tools_3.1.2        
[53] TSP_1.0-10          whisker_0.3-2  

I don't see this problem when loading just Biobase and Heatplus (I guess that is the package where annHeatmap2 is defined?), so try invoking the function in a simpler session. Alternatively, try to identify which of the many packages you have loaded / attached that causes the problem to first appear, and provide the output of traceback() after the error occurs; this might provide enough information to identify what the underlying problem is (superficially, it looks like Heatplus is doing things 'correctly', in terms of package dependencies and imports).