[BioC] PCA-3D Plot
James W. MacDonald
jmacdon at uw.edu
Mon Jul 1 16:05:47 CEST 2013
On 7/1/2013 8:28 AM, Chevala V V S Narayana [guest] wrote:
> 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)
Both princomp() and prcomp() expect the data to be in a conventional
format (with samples in rows and observations in columns). Microarray
data are in general transposed from this format (with observations in
rows and samples in columns), so you need to do
princomp(t(Expresso), cor = TRUE)
Best,
Jim
>> 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
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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