[BioC] PCA-3D Plot

[Chevala V V S Narayana [guest]]

Dear All,

I request help in generating "Sample-based 3D-PCA plot" (Principal component analysis). I used function "princomp" from package:stats to create a PCA object on the data-set. the data dimensions are 600 * 7.

While genetaring, the plot were created on Genes with both "plot3d" and "scatterplot3d" functions, and I want the PCA-3d plot according to the samples.

The code I used is,
> dim(Expresso)
[1] 618   7
> PCA_3d<-princomp(Expresso, cor=TRUE)
> plot3d(PCA_3d$scores[,1:7],xlab="Component 1",main="My 3D 
+ PCA",ylab="Component 2", zlab="Component 3", type="h", box=F, axes=F) 
> spheres3d(PCA_3d$scores[,1:7], radius=0.1, col="pink") 
> grid3d(side="z", at=list(z=0)) 
> text3d(PCA_3d$scores[,1:7], text=rownames(PCA_3d$scores), adj=1.3)

I also tried to plot with function "scatterplot3d"
> scatterplot3d(PCA_3d$scores[,1:3],xlab="Component 1 (26.9%)",main="My 3D PCA",ylab="Component 2(17.9%)", zlab="Component 3 (12.4%)",type="h",box=FALSE,pch=21)

> scatterplot3d(PCA_3d$scores [,1:3],xlab="Component 1 (26.9%)",main="My 3D PCA",ylab="Component 2(17.9%)", zlab="Component 3 (12.4%)",type="h",box=FALSE,pch=21,bg=color)







 -- output of sessionInfo(): 

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] ggplot2_0.9.3        reshape2_1.2.2       scatterplot3d_0.3-33
[4] rgl_0.93.935         DESeq_1.10.1         lattice_0.20-13     
[7] locfit_1.5-8         Biobase_2.18.0       BiocGenerics_0.4.0  

loaded via a namespace (and not attached):
 [1] annotate_1.36.0      AnnotationDbi_1.20.3 colorspace_1.2-1    
 [4] DBI_0.2-5            dichromat_2.0-0      digest_0.6.2        
 [7] genefilter_1.40.0    geneplotter_1.36.0   grid_2.15.1         
[10] gtable_0.1.2         IRanges_1.16.5       labeling_0.1        
[13] MASS_7.3-23          munsell_0.4          parallel_2.15.1     
[16] plyr_1.8             proto_0.3-10         RColorBrewer_1.0-5  
[19] RSQLite_0.11.2       scales_0.2.3         splines_2.15.1      
[22] stats4_2.15.1        stringr_0.6.2        survival_2.37-2     
[25] tcltk_2.15.1         tools_2.15.1         XML_3.95-0.1        
[28] xtable_1.7-0        


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