Sample a flowFrame or flowSet

Source: R/cyto-helpers.R

cyto_sample allows restriction of a flowFrame or flowSet by indicating the percentage or number of events to retain.

cyto_sample(x, ...)

# S3 method for GatingHierarchy
cyto_sample(x, display = 1, seed = NULL, ...)

# S3 method for GatingSet
cyto_sample(x, display = 1, seed = NULL, ...)

# S3 method for flowFrame
cyto_sample(x, display = 1, seed = NULL, ...)

# S3 method for flowSet
cyto_sample(x, display = 1, seed = NULL, ...)

# S3 method for list
cyto_sample(x, display = 1, seed = NULL, plot = FALSE, ...)

Arguments

x

object of class flowFrame, flowSet, GatingHierarchy or GatingSet.
...

not in use.
display

can be either a numeric [0,1] or integer to indicate the percentage or number of events to keep respectively.
seed

value used to set.seed() internally. Setting a value for seed will return the same result with each run.
plot

logical required for lists to indicate whether sampling should be scaled per flowFrame to retain original ratios, as used in cyto_plot.

Value

object of class flowFrame, flowSet, GatingHierarchy or GatingSet sampled to display events.

Author

Dillon Hammill, Dillon.Hammill@anu.edu.au

Examples

# Load in CytoExploreRData to access files
library(CytoExploreRData)

# Load in samples
fs <- Activation

# Restrict first sample by 50%
cyto_sample(fs[[1]], 0.5)

#> flowFrame object 'Activation_1.fcs'
#> with 25000 cells and 18 observables:
#>                   name        desc     range  minRange  maxRange
#> $P1              FSC-A          NA    262144         0    262144
#> $P2              FSC-H          NA    262144         0    262144
#> $P3              FSC-W          NA    262144         0    262144
#> $P4              SSC-A          NA    262144         0    262144
#> $P5              SSC-H          NA    262144         0    262144
#> ...                ...         ...       ...       ...       ...
#> $P14        Qdot 605-A          NA    262144      -111    262144
#> $P15 Alexa Fluor 647-A        CD44    262144      -111    262144
#> $P16 Alexa Fluor 700-A         CD4    262144      -111    262144
#> $P17         APC-Cy7-A       CD11c    262144      -111    262144
#> $P18              Time          NA    262144         0    262144
#> 261 keywords are stored in the 'description' slot

# Restrict first sample to 10000 events
cyto_sample(fs[[1]], 10000)

#> flowFrame object 'Activation_1.fcs'
#> with 10000 cells and 18 observables:
#>                   name        desc     range  minRange  maxRange
#> $P1              FSC-A          NA    262144         0    262144
#> $P2              FSC-H          NA    262144         0    262144
#> $P3              FSC-W          NA    262144         0    262144
#> $P4              SSC-A          NA    262144         0    262144
#> $P5              SSC-H          NA    262144         0    262144
#> ...                ...         ...       ...       ...       ...
#> $P14        Qdot 605-A          NA    262144      -111    262144
#> $P15 Alexa Fluor 647-A        CD44    262144      -111    262144
#> $P16 Alexa Fluor 700-A         CD4    262144      -111    262144
#> $P17         APC-Cy7-A       CD11c    262144      -111    262144
#> $P18              Time          NA    262144         0    262144
#> 261 keywords are stored in the 'description' slot