tests/function_tests/test_fitsne.R

In sydneycytometry/Spectre: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry data.

library('Spectre')
package.check()
package.load()

cell.dat <- Spectre::demo.start
as.matrix(names(cell.dat))
use.cols <- names(cell.dat)[c(2:10)]

cell.dat.1 <- do.asinh(cell.dat, use.cols, cofactor = 1000)
cell.dat.2 <- do.mn(cell.dat, use.cols, asinh.cf = 500, lower.threshold = -2)

make.colour.plot(cell.dat.1, 'CD3_asinh', 'CD4_asinh', filename = 'for test.png')




z.dat <- do.zscore(cell.dat.1, paste0(use.cols, '_asinh'))
z.dat

make.colour.plot(z.dat, 'CD11b_asinh', 'CD45_asinh')
make.colour.plot(z.dat, 'CD3_asinh', 'CD4_asinh')

make.colour.plot(cell.dat.2, 'CD3_transf', 'CD4_transf')








dat.dt <- as.data.table(Spectre::demo.clustered)
dat.df <- as.data.frame(Spectre::demo.clustered)
dat.mt <- as.matrix(Spectre::demo.clustered)

object.size(dat.dt) / 1024 / 1024
object.size(dat.df) / 1024 / 1024
object.size(dat.mt) / 1024 / 1024


x <- dat.df[1:100,]




dat.transf <- do.mn(cell.dat, use.cols, asinh.cf = 1000)
dat.transf


quantile(cell.dat.1$CD3_asinh, 0.005)

make.colour.plot(cell.dat.1, 'CD3_asinh', 'CD4_asinh', 'CD3_asinh')
make.colour.plot(dat.transf, 'CD3_transf', 'CD4_transf', 'CD3_transf')
make.colour.plot(dat.transf, 'CD11b_transf', 'CD45_transf')

dat.transf <- run.flowsom(dat.transf, paste0(use.cols, '_transf'))
dat.transf <- run.fitsne(dat.transf, paste0(use.cols, '_transf'))

make.colour.plot(dat.transf, 'FItSNE_X', 'FItSNE_Y', 'FlowSOM_metacluster', 'factor', add.label = TRUE)