Transform flowstate[['data']]
Arguments
- flowstate.object
A flowstate object as returned from read.flowstate.
- .j
Character vector – default
NULL; any/all parameters having a keyword-value pair ofTYPE/Raw|Unmixed_Fluorescencewill be transformed in[['data']]. If a character vector: specific columns in[['data']]that are to be transformed.- transform.type
Character string – default asinh; quoted function that will be used to transform
.jin[['data']].- cofactor
Numeric – default 5000; if
transform.type= asinh (default), the cofactor will be used to modify the transformation.
Value
UPDATES BY REFERENCE:
flowstate[['data']]; transformed valuesflowstate[['parameters']]; adds two columns ('transform' and 'cofactor')
Invisibly returns the flowstate.object.
Examples
fcs.file.paths <- system.file("extdata", package = "flowstate") |>
list.files(full.names = TRUE, pattern = "BLOCK.*.fcs")
#read .fcs files as a flowstate object; concatenate
fs <- read.flowstate(
fcs.file.paths,
colnames.type="S",
concatenate = TRUE
)
#> COVAIL_002_CYTOKINE_BLOCK1_1.fcs --> flowstate
#> COVAIL_002_CYTOKINE_BLOCK1_2.fcs --> flowstate
#> COVAIL_002_CYTOKINE_BLOCK1_3.fcs --> flowstate
#> Concatenating 'flowstate.ojects'...
#plot and mean values of linear columns
plot(fs,CD3,CD8) + ggplot2::guides(fill = 'none')
#> Warning: Computation failed in `stat_binhex()`.
#> Caused by error in `compute_group()`:
#> ! The package "hexbin" is required for `stat_bin_hex()`.
fs$data[,sapply(.SD,mean),.SDcols = c('CD3','CD4','CD8')]
#> CD3 CD4 CD8
#> 25878.14 19921.68 21843.70
#transform
flowstate.transform(
fs,
.j = c('CD3','CD4','CD8'),
transform.type = "asinh",
cofactor = 5000
)
#> flowstate.object --> transforming...
#updated parameters
fs$parameters[!is.na(transform)]
#> par B DISPLAY E N R S
#> <char> <char> <char> <char> <char> <char> <char>
#> 1: $P16 32 LOG 0,0 BUV805-A 4194304 CD8
#> 2: $P30 32 LOG 0,0 RB744-A 4194304 CD3
#> 3: $P31 32 LOG 0,0 PerCP-Fire 806-A 4194304 CD4
#> TYPE V PROJ N.alias
#> <char> <char> <fctr> <char>
#> 1: Unmixed_Fluorescence 1087 COVAIL_002_CYTOKINE_2025-02-27 BUV805
#> 2: Unmixed_Fluorescence 253 COVAIL_002_CYTOKINE_2025-02-27 RB744
#> 3: Unmixed_Fluorescence 0 COVAIL_002_CYTOKINE_2025-02-27 PerCPFire806
#> S.alias S_N.alias transform cofactor
#> <char> <char> <char> <num>
#> 1: CD8 CD8_BUV805 asinh 5000
#> 2: CD3 CD3_RB744 asinh 5000
#> 3: CD4 CD4_PerCPFire806 asinh 5000
#plot and mean values of transformed columns from updated fs[['data']]
plot(fs,CD3,CD8) + ggplot2::guides(fill = 'none')
#> Warning: Computation failed in `stat_binhex()`.
#> Caused by error in `compute_group()`:
#> ! The package "hexbin" is required for `stat_bin_hex()`.
fs$data[,sapply(.SD,mean),.SDcols = c('CD3','CD4','CD8')]
#> CD3 CD4 CD8
#> 1.8223658 1.6040152 0.9800536
#transform all
flowstate.transform(
fs,
.j = NULL,
transform.type = "asinh",
cofactor = 5000
)
#> flowstate.object --> transforming...
#updated parameters
fs$parameters[!is.na(transform)]
#> par B DISPLAY E N R S
#> <char> <char> <char> <char> <char> <char> <char>
#> 1: $P11 32 LOG 0,0 BUV395-A 4194304 CD45RA
#> 2: $P12 32 LOG 0,0 BUV496-A 4194304 CD45RO
#> 3: $P13 32 LOG 0,0 BUV563-A 4194304 TCRgd
#> 4: $P14 32 LOG 0,0 SBUV605-A 4194304 CD45BC1
#> 5: $P15 32 LOG 0,0 BUV737-A 4194304 IL2
#> 6: $P16 32 LOG 0,0 BUV805-A 4194304 CD8
#> 7: $P17 32 LOG 0,0 BV421-A 4194304 CD197
#> 8: $P18 32 LOG 0,0 Pacific Blue-A 4194304 CD45BC2
#> 9: $P19 32 LOG 0,0 SBV475-A 4194304 CD45BC3
#> 10: $P20 32 LOG 0,0 BV605-A 4194304 CD57
#> 11: $P21 32 LOG 0,0 BV650-A 4194304 CD193
#> 12: $P22 32 LOG 0,0 BV711-A 4194304 CD45BC4
#> 13: $P23 32 LOG 0,0 BV750-A 4194304 CD127
#> 14: $P24 32 LOG 0,0 BV785-A 4194304 CD56
#> 15: $P25 32 LOG 0,0 KIRAVIA Blue 520-A 4194304 CD199
#> 16: $P26 32 LOG 0,0 RB545-A 4194304 CD49a
#> 17: $P27 32 LOG 0,0 RB613-A 4194304 GranzymeB
#> 18: $P28 32 LOG 0,0 PerCP-A 4194304 CD45BC5
#> 19: $P29 32 LOG 0,0 PerCP-eFluor 710-A 4194304 CD95
#> 20: $P30 32 LOG 0,0 RB744-A 4194304 CD3
#> 21: $P31 32 LOG 0,0 PerCP-Fire 806-A 4194304 CD4
#> 22: $P32 32 LOG 0,0 RB780-A 4194304 CD69
#> 23: $P33 32 LOG 0,0 PE-A 4194304 TNFa
#> 24: $P34 32 LOG 0,0 RY586-A 4194304 CD183
#> 25: $P35 32 LOG 0,0 PE-Dazzle 594-A 4194304 IFNg
#> 26: $P36 32 LOG 0,0 PE-Fire 640-A 4194304 CD103
#> 27: $P37 32 LOG 0,0 SBY720-A 4194304 CD45BC6
#> 28: $P38 32 LOG 0,0 PE-Cy7-A 4194304 CD122
#> 29: $P39 32 LOG 0,0 Alexa Fluor 647-A 4194304 ia4b7
#> 30: $P40 32 LOG 0,0 Spark NIR 685-A 4194304 CD45BC7
#> 31: $P41 32 LOG 0,0 LIVE DEAD Scarlet-A 4194304 Viability
#> 32: $P42 32 LOG 0,0 APC-H7-A 4194304 CD27
#> 33: $P43 32 LOG 0,0 APC-Fire 810-A 4194304 KLRG1
#> par B DISPLAY E N R S
#> <char> <char> <char> <char> <char> <char> <char>
#> TYPE V PROJ N.alias
#> <char> <char> <fctr> <char>
#> 1: Unmixed_Fluorescence 258 COVAIL_002_CYTOKINE_2025-02-27 BUV395
#> 2: Unmixed_Fluorescence 523 COVAIL_002_CYTOKINE_2025-02-27 BUV496
#> 3: Unmixed_Fluorescence 535 COVAIL_002_CYTOKINE_2025-02-27 BUV563
#> 4: Unmixed_Fluorescence 0 COVAIL_002_CYTOKINE_2025-02-27 SBUV605
#> 5: Unmixed_Fluorescence 904 COVAIL_002_CYTOKINE_2025-02-27 BUV737
#> 6: Unmixed_Fluorescence 1087 COVAIL_002_CYTOKINE_2025-02-27 BUV805
#> 7: Unmixed_Fluorescence 301 COVAIL_002_CYTOKINE_2025-02-27 BV421
#> 8: Unmixed_Fluorescence 347 COVAIL_002_CYTOKINE_2025-02-27 PacificBlue
#> 9: Unmixed_Fluorescence 0 COVAIL_002_CYTOKINE_2025-02-27 SBV475
#> 10: Unmixed_Fluorescence 330 COVAIL_002_CYTOKINE_2025-02-27 BV605
#> 11: Unmixed_Fluorescence 306 COVAIL_002_CYTOKINE_2025-02-27 BV650
#> 12: Unmixed_Fluorescence 254 COVAIL_002_CYTOKINE_2025-02-27 BV711
#> 13: Unmixed_Fluorescence 327 COVAIL_002_CYTOKINE_2025-02-27 BV750
#> 14: Unmixed_Fluorescence 539 COVAIL_002_CYTOKINE_2025-02-27 BV785
#> 15: Unmixed_Fluorescence 0 COVAIL_002_CYTOKINE_2025-02-27 KIRAVIABlue520
#> 16: Unmixed_Fluorescence 639 COVAIL_002_CYTOKINE_2025-02-27 RB545
#> 17: Unmixed_Fluorescence 369 COVAIL_002_CYTOKINE_2025-02-27 RB613
#> 18: Unmixed_Fluorescence 401 COVAIL_002_CYTOKINE_2025-02-27 PerCP
#> 19: Unmixed_Fluorescence 479 COVAIL_002_CYTOKINE_2025-02-27 PerCPeFluor710
#> 20: Unmixed_Fluorescence 253 COVAIL_002_CYTOKINE_2025-02-27 RB744
#> 21: Unmixed_Fluorescence 0 COVAIL_002_CYTOKINE_2025-02-27 PerCPFire806
#> 22: Unmixed_Fluorescence 616 COVAIL_002_CYTOKINE_2025-02-27 RB780
#> 23: Unmixed_Fluorescence 312 COVAIL_002_CYTOKINE_2025-02-27 PE
#> 24: Unmixed_Fluorescence 312 COVAIL_002_CYTOKINE_2025-02-27 RY586
#> 25: Unmixed_Fluorescence 0 COVAIL_002_CYTOKINE_2025-02-27 PEDazzle594
#> 26: Unmixed_Fluorescence 358 COVAIL_002_CYTOKINE_2025-02-27 PEFire640
#> 27: Unmixed_Fluorescence 0 COVAIL_002_CYTOKINE_2025-02-27 SBY720
#> 28: Unmixed_Fluorescence 296 COVAIL_002_CYTOKINE_2025-02-27 PECy7
#> 29: Unmixed_Fluorescence 159 COVAIL_002_CYTOKINE_2025-02-27 AlexaFluor647
#> 30: Unmixed_Fluorescence 159 COVAIL_002_CYTOKINE_2025-02-27 SparkNIR685
#> 31: Unmixed_Fluorescence 0 COVAIL_002_CYTOKINE_2025-02-27 LIVEDEADScarlet
#> 32: Unmixed_Fluorescence 388 COVAIL_002_CYTOKINE_2025-02-27 APCH7
#> 33: Unmixed_Fluorescence 264 COVAIL_002_CYTOKINE_2025-02-27 APCFire810
#> TYPE V PROJ N.alias
#> <char> <char> <fctr> <char>
#> S.alias S_N.alias transform cofactor
#> <char> <char> <char> <num>
#> 1: CD45RA CD45RA_BUV395 asinh 5000
#> 2: CD45RO CD45RO_BUV496 asinh 5000
#> 3: TCRgd TCRgd_BUV563 asinh 5000
#> 4: CD45BC1 CD45BC1_SBUV605 asinh 5000
#> 5: IL2 IL2_BUV737 asinh 5000
#> 6: CD8 CD8_BUV805 asinh 5000
#> 7: CD197 CD197_BV421 asinh 5000
#> 8: CD45BC2 CD45BC2_PacificBlue asinh 5000
#> 9: CD45BC3 CD45BC3_SBV475 asinh 5000
#> 10: CD57 CD57_BV605 asinh 5000
#> 11: CD193 CD193_BV650 asinh 5000
#> 12: CD45BC4 CD45BC4_BV711 asinh 5000
#> 13: CD127 CD127_BV750 asinh 5000
#> 14: CD56 CD56_BV785 asinh 5000
#> 15: CD199 CD199_KIRAVIABlue520 asinh 5000
#> 16: CD49a CD49a_RB545 asinh 5000
#> 17: GranzymeB GranzymeB_RB613 asinh 5000
#> 18: CD45BC5 CD45BC5_PerCP asinh 5000
#> 19: CD95 CD95_PerCPeFluor710 asinh 5000
#> 20: CD3 CD3_RB744 asinh 5000
#> 21: CD4 CD4_PerCPFire806 asinh 5000
#> 22: CD69 CD69_RB780 asinh 5000
#> 23: TNFa TNFa_PE asinh 5000
#> 24: CD183 CD183_RY586 asinh 5000
#> 25: IFNg IFNg_PEDazzle594 asinh 5000
#> 26: CD103 CD103_PEFire640 asinh 5000
#> 27: CD45BC6 CD45BC6_SBY720 asinh 5000
#> 28: CD122 CD122_PECy7 asinh 5000
#> 29: ia4b7 ia4b7_AlexaFluor647 asinh 5000
#> 30: CD45BC7 CD45BC7_SparkNIR685 asinh 5000
#> 31: Viability Viability_LIVEDEADScarlet asinh 5000
#> 32: CD27 CD27_APCH7 asinh 5000
#> 33: KLRG1 KLRG1_APCFire810 asinh 5000
#> S.alias S_N.alias transform cofactor
#> <char> <char> <char> <num>