Description Usage Arguments Examples
description
1 |
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. |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 | 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))
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.