Function calculates meta-profile(s) from a ScoreMatrix or a ScoreMatrixList, then
produces a heatmap or a set of stacked heatmaps for meta-region profiles
a character that determines central tendency of meta-profile(s).
It takes "mean" (default) or "median".
profile.names
a character vector for names of profiles. If NULL,
the names
will be taken from names(mat) if mat is a
ScoreMatrixList object.
xcoords
a vector of numbers showing relative positions of the bases or
windows. It must match the number of columns in the ScoreMatrix
For example: if there are 2001 elements in the matrices which
are base-pair resolution
and they are centered around an anchor point like TSS, the xcoords
argument should be -1000:1000. This argument is used to plot
accurate x-axis labels for the plots.If NULL it will be equal
to 1:ncol(mat).
col
a vector of color pallete.
color scheme to be used. If NULL, a version of jet colors will be
used.
meta.rescale
if TRUE meta-region profiles are scaled to 0 to 1 range by
subracting the min from profiles and dividing them by
max-min.
winsorize
Numeric vector of two, defaults to c(0,100). This vector
determines the upper and lower percentile values to limit the
extreme values. For example, c(0,99) will limit the values to
only 99th percentile, everything above the 99 percentile will
be equalized to the value of 99th percentile. This is useful
for visualization of matrices that have outliers.
legend.name
a character label plotted next to the legend
cex.legend
A numerical value giving the amount by which
legend axis marks should be magnified relative to the default
xlab
label a character string for x-axis
main
a character string for the plot title
cex.lab
A numerical value giving the amount by which
axis labels (including 'legend.name')
should be magnified relative to the default.
cex.axis
A numerical value giving the amount by which
axis marks should be magnified relative to the default
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(genomation)
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/genomation/heatMeta.Rd_%03d_medium.png", width=480, height=480)
> ### Name: heatMeta
> ### Title: Heatmap for meta-region profiles
> ### Aliases: heatMeta
>
> ### ** Examples
>
> data(cage)
> data(promoters)
> scores1=ScoreMatrix(target=cage,windows=promoters,strand.aware=TRUE)
> data(cpgi)
> scores2=ScoreMatrix(target=cpgi,windows=promoters,strand.aware=TRUE)
>
> x=new("ScoreMatrixList",list(scores1,scores2))
> ## No test:
> heatMeta(mat=x,legend.name="fg",cex.legend=0.8,main="fdf",cex.lab=6,
+ cex.axis=0.9)
>
> ## End(No test)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.