scripts/10b_Boxplots-and-profiles.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)
@

%\section{Boxplots and profiles}
Overview of expressions:

<<>>=
boxplts <- function(minsd=0,maxsd=Inf, maxprof=200){
par(mfrow=c(1,2), mar=c(2,7,1,0), oma=c(1,0,0,0))
x <- t18
boxplot(x,
    horizontal = TRUE, las = 2,
    col = rep(1:(ncol(x)/4),each = 4),
    ylim = range(t18,t19),
    main = 2018,
    cex.axis = 0.75
    )
    nl <- 30
    sds <- apply(x,1,sd)
sel <- which(minsd < sds & sds <= maxsd)
nsel <- length(sel)
if(length(sel) > maxprof) sel <- sel[1:maxprof]
for(i in 1:length(sel))
    lines(x[sel[i],],1:ncol(x) , col=i, lwd=2)
y <- substr(colnames(x),1,1)
abline(h=which(y[-1]!=y[-length(y)])[1]+0.5, col=8, lwd=2, lty=2, xpd=TRUE)
mtext(paste(minsd,"< sd <",maxsd,": n =",length(sel),"/", nsel),1, line=2)
#
x <- t19
boxplot(x,
    horizontal = TRUE, las = 2,
    col = rep(1:(ncol(x)/4),each = 4),
    ylim = range(t18,t19),
    main = 2019,
    cex.axis = 0.75
    )
        sds <- apply(x,1,sd)
sel <- which(minsd < sds & sds < maxsd)
nsel <- length(sel)
if(length(sel) > maxprof) sel <- sel[1:maxprof]
for(i in 1:length(sel))
   lines(x[sel[i],],1:ncol(x) , col=i, lwd=2)
y <- substr(colnames(x),1,1)
abline(h=which(y[-1]!=y[-length(y)])[1]+0.5, col=8, lwd=2, lty=2, xpd=TRUE)
mtext(paste(minsd,"< sd <",maxsd,": n =",length(sel),"/", nsel),1, line=2)
}
@
\clearpage
<<include=FALSE, message=FALSE, warnings=FALSE, cache=FALSE>>=
opts_chunk$set(echo=FALSE)
@
<<>>=
minsd <- 5
maxsd <- Inf
figlbl <- paste("Boxplots with profiles of most variable genes (",
        minsd,
        "< sd <=",
        maxsd,")")
        figlbl
@

<<fig.height=8,fig.cap=figlbl, echo=FALSE>>=
boxplts(minsd,maxsd)
@

The measurements are normalized to similar scales, with a little bit more outliers on the high side (which is not unexpected). In the profiles some switched expressions between varieties can be noticed.

\clearpage

<<>>=
minsd <- 4
maxsd <- 5
figlbl <- paste("Boxplots with profiles of most variable genes (",
        minsd,
        "< sd <=",
        maxsd,")")
@

<<fig.height=8,fig.cap=figlbl, echo=FALSE>>=
boxplts(minsd,maxsd)
@
\clearpage

<<>>=
minsd <- 3
maxsd <- 4
figlbl <- paste("Boxplots with profiles of moderately variable genes (",
        minsd,
        "< sd <",
        maxsd,")")
@

<<fig.height=8,fig.cap=figlbl, echo=FALSE>>=
boxplts(minsd,maxsd)
@

<<>>=
minsd <- 2
maxsd <- 3
figlbl <- paste("Boxplots with profiles of moderately variable genes (",
        minsd,
        "< sd <",
        maxsd,")")
@

<<fig.height=8,fig.cap=figlbl, echo=FALSE>>=
boxplts(minsd,maxsd)
@


<<>>=
minsd <- 1
maxsd <- 2
figlbl <- paste("Boxplots with profiles of low variable genes (",
        minsd,
        "< sd <",
        maxsd,")")
@

<<fig.height=8,fig.cap=figlbl, echo=FALSE>>=
boxplts(minsd,maxsd)
@


<<>>=
minsd <- 0
maxsd <- 1
figlbl <- paste("Boxplots with profiles of least variable genes (",
        minsd,
        "< sd <",
        maxsd,")")
@

<<fig.height=8,fig.cap=figlbl, echo=FALSE>>=
boxplts(minsd,maxsd)
@

<<include=FALSE, message=FALSE, warnings=FALSE, cache=FALSE>>=
opts_chunk$set(echo=TRUE)
@