Nothing
## ----setup, include=FALSE, cache=FALSE-----------------------------------
library(knitr)
options(replace.assign=FALSE,width=50)
opts_chunk$set(fig.path='figure/graphics-',
cache.path='cache/graphics-',
fig.align='center',
dev='pdf', fig.width=5, fig.height=5,
fig.show='hold', cache=FALSE, par=TRUE)
knit_hooks$set(crop=hook_pdfcrop)
knit_hooks$set(par=function(before, options, envir){
if (before && options$fig.show!='none') {
par(mar=c(3,3,2,1),cex.lab=.95,cex.axis=.9,
mgp=c(2,.7,0),tcl=-.01, las=1)
}}, crop=hook_pdfcrop)
## ----include=FALSE-------------------------------------------------------
opts_chunk$set(concordance=TRUE)
## ------------------------------------------------------------------------
x = 5
## ----eval=FALSE, tidy=FALSE----------------------------------------------
## install.packages("nclRcourses",
## repos="http://R-Forge.R-project.org")
## ------------------------------------------------------------------------
library(nclRcourses)
## ------------------------------------------------------------------------
data(yeast_long)
## ------------------------------------------------------------------------
## yeast_long is a data frame
colnames(yeast_long)
## ------------------------------------------------------------------------
colnames(yeast_long)[1]
colnames(yeast_long)[1] = "id"
## ----results='hide'------------------------------------------------------
yeast_long$value
## ----results='hide'------------------------------------------------------
yeast_long[,2]
## ------------------------------------------------------------------------
head(yeast_long$value, 5)
## ----fig.keep='none'-----------------------------------------------------
## Select all measurements on the first probe
d = yeast_long[1:15,]
plot(d$tps, d$value)
## ----test-plot, fig.keep='none'------------------------------------------
plot(d$tps, d$value, xlab="A nice label")
## ----pdf-dev, ref.label='test-plot', dev='pdf', out.width='\\textwidth', echo=FALSE, crop=TRUE----
## ----fig.keep='none'-----------------------------------------------------
plot(d$tps, d$value, col=d$rep)
## ----eval=FALSE, tidy=FALSE----------------------------------------------
## par(mar=c(3,3,2,1), mgp=c(2,.7,0), tck=-.01,
## las=1)
## ----F2, fig.keep="none"-------------------------------------------------
hist(yeast_long$value)
## ----ref.label='F2', dev='pdf', out.width='\\textwidth', echo=FALSE------
## ----fig.keep="none"-----------------------------------------------------
hist(yeast_long$value, breaks="FD")
## ----F3, fig.keep="none"-------------------------------------------------
boxplot(yeast_long$value)
## ----ref.label='F3', out.width='\\textwidth', echo=FALSE-----------------
## ----fig.keep="none"-----------------------------------------------------
boxplot(yeast_long$value ~ yeast_long$type)
## ----tidy=FALSE----------------------------------------------------------
cols = c(rgb(85, 130, 169, alpha=40, maxColorValue=255),
rgb(200, 79, 178, alpha=200, maxColorValue=255))
## ----tidy=FALSE----------------------------------------------------------
par(mar=c(3,3,2,1), mgp=c(2,0.4,0), tck=-.01,
cex.axis=0.9, las=1, xaxs='i', yaxs='i')
## ----f4,tidy=FALSE, fig.keep='none', echo=1:3----------------------------
plot(d[1:5,]$tps, d[1:5, ]$value, type="l", frame=FALSE,
axes=FALSE,
panel.first=abline(h=seq(8.75, 9.5, 0.25),
lwd=3, col="lightgray", lty="dotted"),
xlab="Time", ylab="Expression level",
xlim=c(0, 250), ylim=c(8.5, 9.5),
col=cols[1], lwd=2, cex.lab=0.9)
lines(d[6:10,]$tps, d[6:10, ]$value, col=cols[1], lwd=2)
lines(d[11:15,]$tps, d[11:15, ]$value, col=cols[1], lwd=2)
axis(2, c(8.5, 9, 9.5), c("8.5", "9.0", "9.5"), tick=F, cex.axis=0.8)
axis(1, seq(0, 250, 50), seq(0, 250, 50), cex.axis=0.8)
title("Expression levels of 1769308_at", adj=0,
cex.main=0.9, font.main=2, col.main="black")
lines(seq(0, 240, 60), tapply(d$value, d$tps, mean),
col=cols[2], lwd=2)
## ----ref.label='f4', fig.keep='last', echo=FALSE-------------------------
## ----f4b,eval=FALSE, tidy=FALSE------------------------------------------
## axis(2, c(8.5, 9, 9.5), c("8.5", "9.0", "9.5"), tick=FALSE,
## cex.axis=0.8)
## axis(1, seq(0, 250, 50), seq(0, 250, 50), cex.axis=0.8)
## title("Expression levels of 1769308_at", adj=0,
## cex.main=0.9, font.main=2, col.main="black")
## ----eval=FALSE, tidy=FALSE----------------------------------------------
## lines(seq(0, 240, 60), tapply(d$value, d$tps, mean),
## col=cols[2], lwd=2)
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