highSCREEN (version 0.1)

plotplate: title

Description

description

Usage

plotplate(dat, score="score", main)

Arguments

dat

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

score

Specifies the columns containing the data.

main

Main title for the plot.

Examples

set.seed(1234)

nc = 24
nr = 16

# create 1st triplicate of data matrix with compounds and controls
replicate1 = 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 triplicate of data matrix with compounds and controls
replicate2 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 3rd triplicate of data matrix with compounds and controls
replicate3 = matrix(abs(rnorm(nr*nc)), nr, nc)

# combine all triplicates for the before data
replicates_before = list(replicate1, replicate2, replicate3)
names(replicates_before) = c("Replicate1", "Replicate2", "Replicate3")

# create 1st triplicate of data matrix with compounds and controls
replicate1 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 2nd triplicate of data matrix with compounds and controls
replicate2 = matrix(abs(rnorm(nr*nc)), nr, nc)

# create 3rd triplicate of data matrix with compounds and controls
replicate3 = matrix(abs(rnorm(nr*nc)), nr, nc)

# combine all triplicates for the after data
replicates_after = list(replicate1, replicate2, replicate3)
names(replicates_after) = c("Replicate1", "Replicate2", "Replicate3")

# extract plate 1, triplicate 1
dat11 = extractplate(replicates_before, replicates_after, plate=1, replicate=1)
# extract plate 1, triplicate 2
dat12 = extractplate(replicates_before, replicates_after, plate=1, replicate=2)
# extract plate 1, triplicate 3
dat13 = extractplate(replicates_before, replicates_after, plate=1, replicate=3)

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

# combine 3 triplicates
res1 = rbind(res11, res12, res13)
# reformat result
res1 = formatRESULT(res1, triplicate="Triplicate", score="score", t="Time")

# plot single plate activity levels
plotplate(res1, main="Single Plate Activity Levels")