sigxy.plot {OLIN} | R Documentation |
This function produces a 2D-plot visualizing the significance of spatial bias.
sigxy.plot(Sp,Sn,color.lim=c(-3,3),...)
Sp |
matrix of false discovery rates or p-values for positive deviation of
median/mean of M
as produced by fdrspatial or p.spatial |
Sn |
matrix of false discovery rate or p-values for negative deviation of median/mean of M
as produced by fdrspatial or p.spatial |
color.lim |
limits of color range for plotting vector corresponding to log10(pS ) and log10(nS ) |
... |
Further optional graphical parameter for the image function generating the MXY plot |
The function sigxy.plot
produces a 2d-plot presenting the significance (pS
,nS
)
generated by fdrint
or p.spatial
.
The significance Sp
for positive median/mean of M
of
spatial spot neighbourhoods are presented by red colour; the significance(Sn
) for negative
median/mean of M
of
spatial spot neighbourhoods are presented by green colour.
Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)
colorbar.sig
, fdr.spatial
, p.spatial
, image
,
p.spatial
# To run these examples, "un-comment" them! # # LOADING DATA # data(sw) # # M <- v2m(maM(sw)[,1],Ngc=maNgc(sw),Ngr=maNgr(sw), # Nsc=maNsc(sw),Nsr=maNsr(sw),main="MXY plot of SW-array 1") # # CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS # This can take a while! For testing, you may choose a smaller N. # FDR <- fdr.spatial(M,delta=2,N=100,av="median",edgeNA=TRUE) # sigxy.plot(FDR$FDRp,FDR$FDRn,color.lim=c(-5,5),main="FDR") # # LOADING NORMALISED DATA # data(sw.olin) # M <- v2m(maM(sw.olin)[,1],Ngc=maNgc(sw.olin),Ngr=maNgr(sw.olin), # Nsc=maNsc(sw.olin),Nsr=maNsr(sw.olin),main="MXY plot of SW-array 1") # # CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS # FDR <- fdr.spatial(M,delta=2,N=100,av="median",edgeNA=TRUE) # VISUALISATION OF RESULTS # sigxy.plot(FDR$FDRp,FDR$FDRn,color.lim=c(-5,5),main="FDR") # # # CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS # P <- p.spatial(M,delta=2,N=-1,av="median",p.adjust.method="holm") # VISUALISATION OF RESULTS # sigxy.plot(P$Pp,P$Pn,color.lim=c(-5,5),main="FDR")