highSCREEN (version 0.4)

plotcont: Plot control density

Description

description

Usage

plotcont(dat, score="S", main, xaxis.marks=seq(0,5,0.025))

Arguments

dat

Data frame as an output from \(normplate()\).

score

Specifies the columns containing the data.

main

Main title for the plot.

xaxis.marks

Specifies x-axis mark ticks.

Examples

# NOT RUN {
set.seed(1234)

nc = 24
nr = 16

# create 1st replicate of data matrix with compounds and controls
r1 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create control map
cmap = data.frame(X1=c(rep("Control P", floor(nr/3)), 
rep(c("Control low", "Control med", "Control high"), 
(floor(nr/3)+nr-3*floor(nr/3))/3), rep("Control N", 
floor(nr/3))), X2=c(rep("Control N", floor(nr/3)), 
rep(c("Control low", "Control med", "Control high"), 
(floor(nr/3)+nr-3*floor(nr/3))/3), rep("Control P", floor(nr/3))))
cmap = cmap[seq(1,nr,2),]

# create 2nd replicate of data matrix with compounds and controls
r2 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 3rd replicate of data matrix with compounds and controls
r3 = matrix(abs(rnorm(nr*nc)), nr, nc)

# combine all replicates for the t0-specific data
replicates_t0 = list(r1, r2, r3)
names(replicates_t0) = c("R1", "R2", "R3")

# create 1st replicate of data matrix with compounds and controls
r1 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 2nd replicate of data matrix with compounds and controls
r2 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 3rd replicate of data matrix with compounds and controls
r3 = matrix(abs(rnorm(nr*nc)), nr, nc)

# combine all replicates for the t1-specific data
replicates_t1 = list(r1, r2, r3)
names(replicates_t1) = c("R1", "R2", "R3")

# extract plate 1, replicate 1
dat11 = extractplate(replicates_t0, replicates_t1, plate=1, replicate=1)
# extract plate 1, replicate 2
dat12 = extractplate(replicates_t0, replicates_t1, plate=1, replicate=2)
# extract plate 1, replicate 3
dat13 = extractplate(replicates_t0, replicates_t1, plate=1, replicate=3)

# no normalizion (norm="raw")
res11 = normplate("Main Plate 1", dat11[["dat0"]], dat11[["dat1"]], cmap,
 plate=1, replicate=1, norm="raw")
res12 = normplate("Main Plate 1", dat12[["dat0"]], dat12[["dat1"]], cmap,
 plate=1, replicate=2, norm="raw")
res13 = normplate("Main Pltae 1", dat13[["dat0"]], dat13[["dat1"]], cmap,
 plate=1, replicate=3, norm="raw")

# combine 3 replicates
res1 = rbind(res11, res12, res13)
# reformat result
res1 = formatRESULT(res1, replicate="Replicate", t="Time")

layout(matrix(c(1,2,3), 3, 1, byrow = TRUE))

# plot density of all positive controls
plotcont(subset(res1, welltype=="Control P"), main="Density of Positive Controls",
 xaxis.marks=seq(-1,5,0.025))

# plot density of all negative controls
plotcont(subset(res1, welltype=="Control N"), main="Density of Negative Controls",
 xaxis.marks=seq(-1,5,0.025))

# plot density of controls with low, medium and high concentrations
plotcont(subset(res1, welltype=="Control low" | welltype=="Control med" | 
welltype=="Control high"), main="Density of Controls with Low, 
Medium and High Concentrations", xaxis.marks=seq(-1,5,0.025))
# }