[BioC] Matrix, grid and margin

[James W. MacDonald]

Hi Nicolas,

Grid graphics are not part of Bioconductor, that is a part of base R. So 
you need to ask your questions on R-help.

Best,

Jim



On 7/12/2013 4:51 PM, Servant Nicolas wrote:
> Dear BioC,
>
> I try to do a simple plot based on a grid layout.
> The idea is just to split the layout in a 2x2 grid and plot in each pixel one Matrix.
> The point is that I do not want any margin.
> I try the following code, but it always remains some margins.
> Any experience on this question is welcome !!
> Thank you
> Nicolas
>
>
> ## Top panel
> lc<- 2
> gd<- grid.layout(nrow = lc, ncol = lc,
>                    widths = unit(0.5, "npc"),
>                    heights = unit(0.5, "npc"))
> vp<- viewport(x=0.5, y=0.5, w=unit(1, "npc"), h=unit(1, "npc"), layout=gd)
> pushViewport(vp)
> grid.rect(gp=gpar(col="red"))
>
> ## Matrix plot
> vp<- pushViewport(viewport(x=0.5, y=0.5,w=unit(1, "npc"), h=unit(1, "npc"), layout.pos.row=1, layout.pos.col=1))
> ## At this stage it sounds good ... no margin
> grid.rect(gp=gpar(col="blue"))
>
> ##levelplot of the Matrix
> M<- Matrix(rnorm(100), ncol=10)
>
> nopadding<-list(layout.heights = list(top.padding = 0,
>        main.key.padding = 0,
>            key.axis.padding = 0,
>            axis.xlab.padding = 0,
>            xlab.key.padding = 0,
>            key.sub.padding = 0,
>            bottom.padding = 0),
>            layout.widths = list(left.padding = 0,
>            key.ylab.padding = 0,
>            ylab.axis.padding = 0,
>            axis.key.padding = 0,
>            right.padding = 0))
>
> im<-image(M,colorkey=FALSE,
>        lattice.options=list(par.settings = nopadding),
>        contour=FALSE, scales=list(draw=FALSE),
>        xlab=NULL, ylab=NULL, sub=NULL)
> print(im, vp=vp, newpage=FALSE)
>
> popViewport()
>
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8
>   [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] Matrix_1.0-12   lattice_0.20-15
>
>
> 	[[alternative HTML version deleted]]
>
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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