test-script.R
In plantarum/flowPloidy: Analyze flow cytometer data to determine sample ploidy
library(devtools)
library(flowPloidyData)
load_all()
batch1 <- batchFlowHist(flowPloidyFiles, channel="FL3.INT.LIN",
standards = 2.5)
batch1 <- batchFlowHist(flowPloidyFiles, channel="FL3.INT.LIN")
endo <- FlowHist(file = "~/research/flow/problems/endopolyploidy.LMD",
channel = "FL3.INT.LIN", g2 = FALSE)
etFiles <- list.files("~/research/flow/problems/etienne/",
pattern = ".fcs", full.names = TRUE)
viewFlowChannels(etFiles[1])
etienne <- batchFlowHist(etFiles, channel = "FL3.A", standard = 2.5)
et <- browseFlowHist(etienne)
etienne <- FlowHist(file = "~/research/flow/problems/etienne/",
channel = "FL3.INT.LIN", g2 = FALSE)
b1 <- batch1[[1]]
b1Br <- browseFlowHist(batch1)
b3 <- b1Br[[3]]
nuria <- FlowHist(file = "~/research/flow/nuria.fcs", channel = "DAPI.A",
g2 = FALSE, debrisLimit = 10, samples = 5)
fhWMean <- function(fh, range){
sum(fhHistData(fh)$intensity[range] * range) /
sum(fhHistData(fh)$intensity[range])
}
fhVisual <- function(fh, range){
dat <- rep(range, times = fhHistData(fh)$intensity[range])
message("Mean: ", mean(dat))
message("CV: ", sd(dat)/ mean(dat))
message("counts: ", length(dat))
}
svg(filename = "visual_gate.svg", width = 25/2.54, height = 25*0.66/2.54,
family = "lato")
par(mar = c(5,5, 1, 1))
plot(b1Br[[11]], nls = FALSE, init = FALSE, comps= FALSE, main = "",
xlim = c(0, 175))
rcol = "#FF000060"
rect(xleft = 42, xright = 47, ybottom = 0, ytop=300, col = rcol,
border = rcol)
rect(xleft = 55, xright = 60, ybottom = 0, ytop=300, col = rcol,
border = rcol)
rect(xleft = 125, xright = 133, ybottom = 0, ytop=300, col = rcol,
border = rcol)
rect(xleft = 144, xright = 152, ybottom = 0, ytop=300, col = rcol,
border = rcol)
dev.off()
svg(filename = "nls_fit.svg", width = 25/2.54, height = 25*0.66/2.54,
family = "lato")
#dev.new(width = 25/2.54, height = 25 * 0.66/2.54)
par(mar = c(5,5, 1, 1))
plot(b1Br[[11]], nls = TRUE, init = FALSE, comps= TRUE, main = "",
xlim = c(0, 175))
dev.off()
svg(filename = "endo.svg", width = 25/2.54, height = 25*0.66/2.54,
family = "lato")
#dev.new(width = 25/2.54, height = 25 * 0.66/2.54)
par(mar = c(5,5, 1, 1))
plot(endo, nls = TRUE, init = FALSE, comps= TRUE, main = "",
xlim = c(0, 125))
dev.off()
abline(v = 42)
abline(v = 47)
abline(v = 55)
abline(v = 60)
fhVisual(b1Br[[11]], 42:60)
fhVisual(b1Br[[11]], 47:55)
fhVisual(b1Br[[11]], 42:55)
fhVisual(b1Br[[11]], 47:60)
## mean range from 49.8 to 51.5
## CV range from 7.3% to 4.0%
## counts range from 1883 to 1475
abline(v = 125)
abline(v = 133)
abline(v = 144)
abline(v = 152)
fhVisual(b1Br[[11]], 125:152)
fhVisual(b1Br[[11]], 133:144)
fhVisual(b1Br[[11]], 125:144)
fhVisual(b1Br[[11]], 133:152)
## mean range from 137.4 to 139.4
## CV range from 2.1% to 3.6%
## counts range from 1664 to 2126
## ratio ranges from 0.357 to 0.37
## with a standard size of 3 pg, this translates to a range of 0.05 pg,
## introduce 5% or more variation due to subjectivity
browseFlowHist(nuria)
chh <- FlowHist(file = "~/research/flow/problems/valentin/chh101.fcs",
channel = "FL4.A", standards = 1.99)
chc <- FlowHist(file = "~/research/flow/problems/valentin/chc203.fcs",
channel = "FL4.A", standards = 1.99, debrisLimit = 0)
viewFlowChannels("~/research/flow/sample.001.fcs")
brian <- FlowHist("~/research/flow/problems/brian/sample.001.fcs",
channel = "FL2.A", samples = 1)
library(digest)
digest(brian@histData$intensity, "md5")
# [1] "f0724874dd1beeb6bb5e20fac8e3de5e"
brian@raw@description$`$DATE`
# [1] "17-Jan-18"
brian@raw@description$`$BTIM`
# [1] "17:11:47"
brian@raw@description$`FILE GUID`
# [1] "8E581367-FBEC-11E7-AE75-001124882388"
lowPeaks <- list.files("/home/tws/research/flow/paul/low-peaks",
full.names = TRUE)
low <- batchFlowHist(lowPeaks, channel= "FL2.A", debrisLimit = 10)
low <- browseFlowHist(low)
badFiles <- list.files("/home/tws/research/flow/paul/badFiles", full.names
= TRUE)
fpBad <- badFiles[8]
bad <- batchFlowHist(badFiles, channel = "FL2.A")
bad <- browseFlowHist(bad)
etienne <- batchFlowHist(list.files("/home/tws/research/flow/etienne/",
full.names = TRUE),
channel = "FL3.INT.LIN", standards = 2.5)
etBr <- browseFlowHist(etienne)
e1 <- FlowHist("Calli+laxa-moved gate 2017-02-07 553.LMD",
channel = "FL3.INT.LIN")
e1 <- FlowHist("Calliciprus+laxa 2017-02-07 550.LMD",
channel = "FL3.INT.LIN")
e1 <- FlowHist("call1.LMD", channel = "FL3.INT.LIN")
viewFlowChannels("~/research/flow/160930_HCT116_Ca-new.fcs")
viewFlowChannels("~/research/flow/160930_HCT116_Ca.fcs")
hct <- FlowHist("~/research/flow/160930_HCT116_Ca-new.fcs",
channel = "Propidium.Iodide.A")
hctB <- browseFlowHist(hct)
hctNoDebris <- dropComponents(hct, c("SC", "AG"))
hctNoDebris <- fhAnalyze(hctNoDebris)
plot(hctNoDebris, ylim = c(0, 800))
browseFlowHist(hct)
browseFlowHist(hctNoDebris)
plot(hct, ylim = c(0, 800))
hct <- FlowHist("~/research/flow/160930_HCT116_Ca-new.fcs",
channel = "Propidium.Iodide.A", bins = 512)
batch1 <- batchFlowHist(flowPloidyFiles, channel="FL3.INT.LIN",
standards = 2.5)
b1 <- batch1[[1]]
b1Br <- browseFlowHist(batch1)
b1 <- batch1[[1]]
do.call(integrate, c(substitute(fhModel(b1)), as.list(coef(fhNLS(b1))),
lower = 0, upper = 256, subdivisions = 512,
SCvals = substitute(fhHistData(b1)["SCvals"]),
DBvals = substitute(fhHistData(b1)["DBvals"]),
TRvals = substitute(fhHistData(b1)["TRvals"]),
QDvals = substitute(fhHistData(b1)["QDvals"])))
integrate(fhModel(b1),
a1 = coef(fhNLS(b1))["a1"],
Ma = coef(fhNLS(b1))["Ma"],
Sa = coef(fhNLS(b1))["Sa"],
a2 = coef(fhNLS(b1))["a2"],
d = coef(fhNLS(b1))["d"],
BRA = coef(fhNLS(b1))["BRA"],
b1 = coef(fhNLS(b1))["b1"],
Mb = coef(fhNLS(b1))["Mb"],
Sb = coef(fhNLS(b1))["Sb"],
SCa = coef(fhNLS(b1))["SCa"],
SCvals = fhHistData(b1)["SCvals"],
Ap = coef(fhNLS(b1))["Ap"],
DBvals = fhHistData(b1)["DBvals"],
TRvals = fhHistData(b1)["TRvals"],
QDvals = fhHistData(b1)["QDvals"],
lower = 0, upper = 256, subdivisions = 1000)
b1b <- browseFlowHist(batch1)
vac2 <-
FlowHist(
file = "~/research/flow/gating examples/Vac.ON.DL.14.026",
channel = "FL2.A")
browseFlowHist(vac2)
vac2ND <- dropComponents(vac2, c("SC", "AG"))
vac2NDAn <- browseFlowHist(vac2ND)
dat <- exprs(fhRaw(vac2))
thresh <- 0.05
test <- dat[ , "FL3.H"]/ dat[, "FL2.A"] < thresh
vac2g <- setGate(vac2, test)
## vac2g <- cleanPeaks(findPeaks(vac2g))
vac2g <- pickPeaks(vac2g)
vac2g <- addComponents(vac2g)
vac2g <- setLimits(vac2g)
vac2g <- makeModel(vac2g)
vac2g <- getInit(vac2g)
vac2g <- fhAnalyze(vac2g)
par(mfrow=c(2,2))
plot(vac2, sub = "ungated")
plot(dat[, "FL2.A"], dat[ , "FL3.H"]/ dat[, "FL2.A"], pch = 16,
ylim = c(0, 0.08),
col = "#11111130", cex = 0.5, main = fhFile(vac2))
abline(h = thresh, col = 2)
plot(vac2g, sub = "gated")
plotResid(vac2g)
## SSC plots
thresh <- 1
test <- dat[ , "SSC.H"]/ dat[, "FL2.A"] < thresh
vac2g <- setGate(vac2, test)
## vac2g <- cleanPeaks(findPeaks(vac2g))
vac2g <- pickPeaks(vac2g)
vac2g <- addComponents(vac2g)
vac2g <- setLimits(vac2g)
vac2g <- makeModel(vac2g)
vac2g <- getInit(vac2g)
vac2g <- fhAnalyze(vac2g)
par(mfrow=c(2,2))
plot(vac2, sub = "ungated")
plot(dat[, "FL2.A"], dat[ , "SSC.H"]/ dat[, "FL2.A"], pch = 16,
ylim = c(0, 3),
col = "#11111130", cex = 0.5, main = fhFile(vac2))
abline(h = thresh, col = 2)
plot(vac2g, sub = "gated")
plotResid(vac2g)
vac2g <- fhAnalyze(vac2g)
vac2gd <- dropComponents(vac2g, c("SC", "MC"))
vac2gd <- fhAnalyze(vac2gd)
vac2g <- findPeaks(vac2g)
vac2g <- cleanPeaks(vac2g, window = 20)
vac2g <- addComponents(vac2g)
vac2g <- makeModel(vac2g)
vac2g <- getInit(vac2g)
vac2g <- pickInit(vac2g)
plot(vac2g, init = TRUE)
thresh = 0.0002
par(mfrow = c(2,2))
deb <- batch1[["240+S.LMD"]]
debm <- batch1[["240+S.LMD"]]
debm2 <- batch1[["240+S.LMD"]]
plot(deb)
sscfl <- exprs(fhRaw(deb))[, "SS.INT.LIN"] /
exprs(fhRaw(deb))[, "FL3.INT.LIN"]
fl <- exprs(fhRaw(deb))[, "FL3.INT.LIN"]
plot(sscfl ~ fl, col = "#44444411", pch = 16, ylim = c(0, 0.1))
dat <- as.data.frame(exprs(fhRaw(deb)))
dat$ssfl <- sscfl
abline(h = thresh, col = 2)
dat1 <- dat[dat$ssfl > thresh, ]
dat2 <- dat[dat$ssfl <= thresh, ]
debm@raw@exprs <- as.matrix(dat1)
debm2@raw@exprs <- as.matrix(dat2)
debm <- setBins(debm)
debm2 <- setBins(debm2)
plot(debm)
plot(debm2)
plantarum/flowPloidy documentation built on March 25, 2023, 1:37 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library(devtools)
library(flowPloidyData)
load_all()
batch1 <- batchFlowHist(flowPloidyFiles, channel="FL3.INT.LIN",
standards = 2.5)
batch1 <- batchFlowHist(flowPloidyFiles, channel="FL3.INT.LIN")
endo <- FlowHist(file = "~/research/flow/problems/endopolyploidy.LMD",
channel = "FL3.INT.LIN", g2 = FALSE)
etFiles <- list.files("~/research/flow/problems/etienne/",
pattern = ".fcs", full.names = TRUE)
viewFlowChannels(etFiles[1])
etienne <- batchFlowHist(etFiles, channel = "FL3.A", standard = 2.5)
et <- browseFlowHist(etienne)
etienne <- FlowHist(file = "~/research/flow/problems/etienne/",
channel = "FL3.INT.LIN", g2 = FALSE)
b1 <- batch1[[1]]
b1Br <- browseFlowHist(batch1)
b3 <- b1Br[[3]]
nuria <- FlowHist(file = "~/research/flow/nuria.fcs", channel = "DAPI.A",
g2 = FALSE, debrisLimit = 10, samples = 5)
fhWMean <- function(fh, range){
sum(fhHistData(fh)$intensity[range] * range) /
sum(fhHistData(fh)$intensity[range])
}
fhVisual <- function(fh, range){
dat <- rep(range, times = fhHistData(fh)$intensity[range])
message("Mean: ", mean(dat))
message("CV: ", sd(dat)/ mean(dat))
message("counts: ", length(dat))
}
svg(filename = "visual_gate.svg", width = 25/2.54, height = 25*0.66/2.54,
family = "lato")
par(mar = c(5,5, 1, 1))
plot(b1Br[[11]], nls = FALSE, init = FALSE, comps= FALSE, main = "",
xlim = c(0, 175))
rcol = "#FF000060"
rect(xleft = 42, xright = 47, ybottom = 0, ytop=300, col = rcol,
border = rcol)
rect(xleft = 55, xright = 60, ybottom = 0, ytop=300, col = rcol,
border = rcol)
rect(xleft = 125, xright = 133, ybottom = 0, ytop=300, col = rcol,
border = rcol)
rect(xleft = 144, xright = 152, ybottom = 0, ytop=300, col = rcol,
border = rcol)
dev.off()
svg(filename = "nls_fit.svg", width = 25/2.54, height = 25*0.66/2.54,
family = "lato")
#dev.new(width = 25/2.54, height = 25 * 0.66/2.54)
par(mar = c(5,5, 1, 1))
plot(b1Br[[11]], nls = TRUE, init = FALSE, comps= TRUE, main = "",
xlim = c(0, 175))
dev.off()
svg(filename = "endo.svg", width = 25/2.54, height = 25*0.66/2.54,
family = "lato")
#dev.new(width = 25/2.54, height = 25 * 0.66/2.54)
par(mar = c(5,5, 1, 1))
plot(endo, nls = TRUE, init = FALSE, comps= TRUE, main = "",
xlim = c(0, 125))
dev.off()
abline(v = 42)
abline(v = 47)
abline(v = 55)
abline(v = 60)
fhVisual(b1Br[[11]], 42:60)
fhVisual(b1Br[[11]], 47:55)
fhVisual(b1Br[[11]], 42:55)
fhVisual(b1Br[[11]], 47:60)
## mean range from 49.8 to 51.5
## CV range from 7.3% to 4.0%
## counts range from 1883 to 1475
abline(v = 125)
abline(v = 133)
abline(v = 144)
abline(v = 152)
fhVisual(b1Br[[11]], 125:152)
fhVisual(b1Br[[11]], 133:144)
fhVisual(b1Br[[11]], 125:144)
fhVisual(b1Br[[11]], 133:152)
## mean range from 137.4 to 139.4
## CV range from 2.1% to 3.6%
## counts range from 1664 to 2126
## ratio ranges from 0.357 to 0.37
## with a standard size of 3 pg, this translates to a range of 0.05 pg,
## introduce 5% or more variation due to subjectivity
browseFlowHist(nuria)
chh <- FlowHist(file = "~/research/flow/problems/valentin/chh101.fcs",
channel = "FL4.A", standards = 1.99)
chc <- FlowHist(file = "~/research/flow/problems/valentin/chc203.fcs",
channel = "FL4.A", standards = 1.99, debrisLimit = 0)
viewFlowChannels("~/research/flow/sample.001.fcs")
brian <- FlowHist("~/research/flow/problems/brian/sample.001.fcs",
channel = "FL2.A", samples = 1)
library(digest)
digest(brian@histData$intensity, "md5")
# [1] "f0724874dd1beeb6bb5e20fac8e3de5e"
brian@raw@description$`$DATE`
# [1] "17-Jan-18"
brian@raw@description$`$BTIM`
# [1] "17:11:47"
brian@raw@description$`FILE GUID`
# [1] "8E581367-FBEC-11E7-AE75-001124882388"
lowPeaks <- list.files("/home/tws/research/flow/paul/low-peaks",
full.names = TRUE)
low <- batchFlowHist(lowPeaks, channel= "FL2.A", debrisLimit = 10)
low <- browseFlowHist(low)
badFiles <- list.files("/home/tws/research/flow/paul/badFiles", full.names
= TRUE)
fpBad <- badFiles[8]
bad <- batchFlowHist(badFiles, channel = "FL2.A")
bad <- browseFlowHist(bad)
etienne <- batchFlowHist(list.files("/home/tws/research/flow/etienne/",
full.names = TRUE),
channel = "FL3.INT.LIN", standards = 2.5)
etBr <- browseFlowHist(etienne)
e1 <- FlowHist("Calli+laxa-moved gate 2017-02-07 553.LMD",
channel = "FL3.INT.LIN")
e1 <- FlowHist("Calliciprus+laxa 2017-02-07 550.LMD",
channel = "FL3.INT.LIN")
e1 <- FlowHist("call1.LMD", channel = "FL3.INT.LIN")
viewFlowChannels("~/research/flow/160930_HCT116_Ca-new.fcs")
viewFlowChannels("~/research/flow/160930_HCT116_Ca.fcs")
hct <- FlowHist("~/research/flow/160930_HCT116_Ca-new.fcs",
channel = "Propidium.Iodide.A")
hctB <- browseFlowHist(hct)
hctNoDebris <- dropComponents(hct, c("SC", "AG"))
hctNoDebris <- fhAnalyze(hctNoDebris)
plot(hctNoDebris, ylim = c(0, 800))
browseFlowHist(hct)
browseFlowHist(hctNoDebris)
plot(hct, ylim = c(0, 800))
hct <- FlowHist("~/research/flow/160930_HCT116_Ca-new.fcs",
channel = "Propidium.Iodide.A", bins = 512)
batch1 <- batchFlowHist(flowPloidyFiles, channel="FL3.INT.LIN",
standards = 2.5)
b1 <- batch1[[1]]
b1Br <- browseFlowHist(batch1)
b1 <- batch1[[1]]
do.call(integrate, c(substitute(fhModel(b1)), as.list(coef(fhNLS(b1))),
lower = 0, upper = 256, subdivisions = 512,
SCvals = substitute(fhHistData(b1)["SCvals"]),
DBvals = substitute(fhHistData(b1)["DBvals"]),
TRvals = substitute(fhHistData(b1)["TRvals"]),
QDvals = substitute(fhHistData(b1)["QDvals"])))
integrate(fhModel(b1),
a1 = coef(fhNLS(b1))["a1"],
Ma = coef(fhNLS(b1))["Ma"],
Sa = coef(fhNLS(b1))["Sa"],
a2 = coef(fhNLS(b1))["a2"],
d = coef(fhNLS(b1))["d"],
BRA = coef(fhNLS(b1))["BRA"],
b1 = coef(fhNLS(b1))["b1"],
Mb = coef(fhNLS(b1))["Mb"],
Sb = coef(fhNLS(b1))["Sb"],
SCa = coef(fhNLS(b1))["SCa"],
SCvals = fhHistData(b1)["SCvals"],
Ap = coef(fhNLS(b1))["Ap"],
DBvals = fhHistData(b1)["DBvals"],
TRvals = fhHistData(b1)["TRvals"],
QDvals = fhHistData(b1)["QDvals"],
lower = 0, upper = 256, subdivisions = 1000)
b1b <- browseFlowHist(batch1)
vac2 <-
FlowHist(
file = "~/research/flow/gating examples/Vac.ON.DL.14.026",
channel = "FL2.A")
browseFlowHist(vac2)
vac2ND <- dropComponents(vac2, c("SC", "AG"))
vac2NDAn <- browseFlowHist(vac2ND)
dat <- exprs(fhRaw(vac2))
thresh <- 0.05
test <- dat[ , "FL3.H"]/ dat[, "FL2.A"] < thresh
vac2g <- setGate(vac2, test)
## vac2g <- cleanPeaks(findPeaks(vac2g))
vac2g <- pickPeaks(vac2g)
vac2g <- addComponents(vac2g)
vac2g <- setLimits(vac2g)
vac2g <- makeModel(vac2g)
vac2g <- getInit(vac2g)
vac2g <- fhAnalyze(vac2g)
par(mfrow=c(2,2))
plot(vac2, sub = "ungated")
plot(dat[, "FL2.A"], dat[ , "FL3.H"]/ dat[, "FL2.A"], pch = 16,
ylim = c(0, 0.08),
col = "#11111130", cex = 0.5, main = fhFile(vac2))
abline(h = thresh, col = 2)
plot(vac2g, sub = "gated")
plotResid(vac2g)
## SSC plots
thresh <- 1
test <- dat[ , "SSC.H"]/ dat[, "FL2.A"] < thresh
vac2g <- setGate(vac2, test)
## vac2g <- cleanPeaks(findPeaks(vac2g))
vac2g <- pickPeaks(vac2g)
vac2g <- addComponents(vac2g)
vac2g <- setLimits(vac2g)
vac2g <- makeModel(vac2g)
vac2g <- getInit(vac2g)
vac2g <- fhAnalyze(vac2g)
par(mfrow=c(2,2))
plot(vac2, sub = "ungated")
plot(dat[, "FL2.A"], dat[ , "SSC.H"]/ dat[, "FL2.A"], pch = 16,
ylim = c(0, 3),
col = "#11111130", cex = 0.5, main = fhFile(vac2))
abline(h = thresh, col = 2)
plot(vac2g, sub = "gated")
plotResid(vac2g)
vac2g <- fhAnalyze(vac2g)
vac2gd <- dropComponents(vac2g, c("SC", "MC"))
vac2gd <- fhAnalyze(vac2gd)
vac2g <- findPeaks(vac2g)
vac2g <- cleanPeaks(vac2g, window = 20)
vac2g <- addComponents(vac2g)
vac2g <- makeModel(vac2g)
vac2g <- getInit(vac2g)
vac2g <- pickInit(vac2g)
plot(vac2g, init = TRUE)
thresh = 0.0002
par(mfrow = c(2,2))
deb <- batch1[["240+S.LMD"]]
debm <- batch1[["240+S.LMD"]]
debm2 <- batch1[["240+S.LMD"]]
plot(deb)
sscfl <- exprs(fhRaw(deb))[, "SS.INT.LIN"] /
exprs(fhRaw(deb))[, "FL3.INT.LIN"]
fl <- exprs(fhRaw(deb))[, "FL3.INT.LIN"]
plot(sscfl ~ fl, col = "#44444411", pch = 16, ylim = c(0, 0.1))
dat <- as.data.frame(exprs(fhRaw(deb)))
dat$ssfl <- sscfl
abline(h = thresh, col = 2)
dat1 <- dat[dat$ssfl > thresh, ]
dat2 <- dat[dat$ssfl <= thresh, ]
debm@raw@exprs <- as.matrix(dat1)
debm2@raw@exprs <- as.matrix(dat2)
debm <- setBins(debm)
debm2 <- setBins(debm2)
plot(debm)
plot(debm2)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.