sigxy.plot2 {OLIN} | R Documentation |
This function produces a 2D-plot visualizing the significance of spatial bias.
sigxy.plot2(object,Sp,Sn,color.lim=c(-3,3),...)
object |
object of class marrayRaw or marrayNorm |
Sp |
vector of false discovery rates or p-values for positive deviation of
median/mean of M
as produced by fdrspatial or p.spatial |
Sn |
vector 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.plot2
differs from sigxy.plot
in its input arguments.
The functionality is the same. For details, see sigxy.plot
.
This function will be merged with sigxy.plot
in future versions.
Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)
colorbar.sig
, sigxy.plot
,
\code{sigxy.plot},fdr.spatial2
, p.spatial2
, image
# To run these examples, "un-comment" them! # # LOADING DATA # data(sw) # CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS # For this illustration, N was chosen rather small. For "real" analysis, it should be larger. # FDR <- fdr.spatial2(sw,delta=2,N=10,av="median",edgeNA=TRUE) # # SIGNIFICANCE PLOTS OF ARRAY 1 # sigxy.plot2(sw[,1],FDR$FDRp[[1]],FDR$FDRn[[1]],color.lim=c(-5,5),main="FDR") # SIGNIFICANCE PLOTS OF ARRAY 3 # sigxy.plot2(sw[,3],FDR$FDRp[[3]],FDR$FDRn[[3]],color.lim=c(-5,5),main="FDR") #