scripts/55aa_one-gene-plots.Rnw

Version 1

% -*- TeX:Rnw:UTF-8 -*-
% ----------------------------------------------------------------
% .R knitr file  ************************************************
% ----------------------------------------------------------------
%%
<<echo=FALSE>>=
###############################################
##                                           ##
## (c) Andrej Blejec (andrej.blejec@nib.si)  ##
##                                           ##
###############################################
@
<<echo=FALSE,results='hide'>>=
options(width=70)
pc <- stat4[varname,"P.value.c"]
pfc <- stat4[varname,"P.value.f.c"]
inc <- c(" ","*")[(pc < alpha)+1]
incf <- c(" ","+")[((pc > alpha)&(pfc < alpha))+1]
@

\clearpage
\subsubsection{ \Sexpr{varname}: \Sexpr{df4[varname,typevar]} \Sexpr{inc}\Sexpr{incf} }

<<echo=FALSE,eval=FALSE,include=FALSE>>=
varname
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<<>>=
#cat.feature(fdata[fdata$geneID %in% varname,2:5])
cat.feature(mfdata[varname,])
@

Coefficients  for \Sexpr{varname}.

<<echo=FALSE>>=
fill <- function(x, n=1, sep=" "){
    ns <- nchar(x)
    ns <- max(ns)-ns+n
    fills <- paste(rep(sep,20),collapse="")
    for(i in 1:length(x))
    x[i] <- paste0(x[i],substr(fills,1,ns[i]))
x
}
@

<<echo=FALSE>>=
p.stars <- function(x, legend=FALSE, ...){
   Signif <- symnum(x
  , corr = FALSE, na = FALSE,
                cutpoints = c(0, 0.001, 0.01, 0.05, 0.1, 1),
                symbols = c("***", "**", "*", ".", " "),
                legend = legend,
                 ...)
Signif
}
@

<<eval=FALSE, echo=FALSE, results="hide">>=
pp <- unlist(x[,2])
pp0 <- c(0.1,0.001,0.05)
pp0 <- c(1.426785e-01 ,7.199473e-01 ,5.286929e-01)
pp
Signif <- NULL
as.character(p.stars(pp0))
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<<echo=FALSE>>=
## tt[varname,]  # is the same as in stat4
cn <- colnames(stat4)
idc <- grep("Coef",cn)
idp <- grep("P.value",cn)
x <- data.frame(matrix(stat4[varname,c(idc,idp)],ncol=3,
    dimnames=list(cn[idc],c("Value","P.value","P.value.adj")))
)
signif <- p.stars(unlist(x[,2]))
x$sig <- as.list(signif)
x$sig.adj <- as.list(p.stars(unlist(x[,3])))
x <- x[,c(1:2,4,3,5)]
cdesc <- c("MeanC", "SlopeC", "MeanF-MeanC", "SlopeF-SlopeC")

#rownames(x) <- paste(fill(rownames(x)),cdesc)
rownames(x) <-  cdesc
#printCoefmat(x, has.Pvalue=TRUE)
x
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<<echo=FALSE>>=
opts_chunk$set( fig.path=paste0('./figs/55-',varname,"-") )
@

<<echo=FALSE>>=
#par(mfrow=c(2,3))
#
#plot.wpe(varname,model="")
#plot.wpe(varname,model="+")
#plot.wpe(varname,model="*")
a <- plot.ewp(varname,model="", , exprs=exprs, pd=pd, ylim=range(exprs)
     , cex= 1.5
     , pch = c(16,16)
     , all = FALSE
     )
mtext(paste(round(coefs[varname,],1),collapse=" | "),cex=0.75)
abline(v= -1.4, col=8, lty=2)
#plot.ewp(varname,model="+")
#plot.ewp(varname,model="*")
#r2 <- summary(fits[["all"]])$r.squared
@

<<echo=FALSE>>=
opts_chunk$set( fig.path='./figs/50-' )
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