countItems: Manually counting the number of cells in colonies

Description Usage Arguments Details Value See Also Examples

Description

Display the profile and the image of each particle and allow the user to manually count the number of cells by simple left-clicking on each of them.

Usage

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countItems(profile, feature = NULL, imgdir = NULL, image = NULL)

Arguments

profile

matrix of profile data (signals in columns).

feature

vector of features data.

imgdir

character vector specifying the path of the images directory.

image

character vector specifying the name of the considered image in imgdir.

Details

countItems displays the profile and the image of each particle and allows the user to manually count the number of cells by simple left-clicking on each of them

Value

nbItemsTot number of cells manually counted on each image.

See Also

itemsModel, computeItems

Examples

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dat <- rbind(matrix(rnorm(100, mean = 2, sd = 0.3), ncol = 2), 
             matrix(rnorm(100, mean = 4, sd = 0.3), ncol = 2), 
             matrix(rnorm(100, mean = 6, sd = 0.3), ncol = 2))
colnames(dat) <- c("x","y")
tf1 <- tempfile()
write.table(dat, tf1, sep=",", dec=".")

sig <- data.frame(ID=rep(1:150, each=30), SIGNAL=rep(dnorm(seq(-2,2,length=30)),150))
tf2 <- tempfile()
write.table(sig, tf2, sep=",", dec=".")

x <- importSample(file.features=tf1, file.profiles=tf2, dir.save=tempdir())

nbItems <- countItems(x$profiles[[1]])

RclusTool documentation built on Feb. 4, 2020, 5:08 p.m.