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library(Luciernaga)
library(dplyr)
TheUnstained <- read.csv("data/Unstained4L.csv", check.names=FALSE)
TheUnstained <- TheUnstained |> select(-Experiment, -Condition, -Count, -Sample) |> slice(1)
Unstained <- TheUnstained
Panel <- file.path("data", "Panel.csv")
Panel <- read.csv(Panel, check.names=FALSE) |> dplyr::filter(Day %in% c(1,2,3,4,5))
GT <- FluorophoreMatrix(data=Panel, NumberDetectors = 54)| D | WV | Fluorophore | Antigen | D | Fluorophore | Antigen | D | Fluorophore | Antigen |
|---|---|---|---|---|---|---|---|---|---|
| V1 | 428 | BV421 | CD62L | ||||||
| V2 | 443 | ||||||||
| V3 | 458 | Pacific Blue | B220 | ||||||
| V4 | 473 | ||||||||
| V5 | 508 | BV480 | CD11b | B1 | |||||
| V6 | 525 | B2 | FITC | MHC II | |||||
| V7 | 542 | BV510 | CD8 | B3 | Spark Blue 550 | CD3 | |||
| V8 | 581 | BV570 | Ly6C | B4 | PE | F4-80 | |||
| V9 | 598 | B5 | |||||||
| V10 | 615 | BV605 | CD4 | B6 | |||||
| V11 | 662 | BV650 | CD317 | B7 | 7-AAD | Viability | R1 | APC | CD44 |
| 679 | B8 | PE-Cy5 | CD25 | R2 | |||||
| V12 | 695 | B9 | PerCP-Cy5.5 | CD11c | R3 | ||||
| V13 | 718 | BV711 | Ly6G | B10 | R4 | Alexa Fluor 700 | CD45 | ||
| 738 | B11 | R5 | |||||||
| V14 | 750 | ||||||||
| 760 | B12 | R6 | |||||||
| V15 | 781 | BV785 | CD127 | B13 | PE-Cy7 | PD-1 | R7 | APC-Fire 750 | LAG-3 |
| V16 | 812 | B14 | R8 | APC-Fire 810 | NK1.1 |
TheFluorophores <- FluorophoreMatrix(data=Panel, NumberDetectors = 54,
returnType="data") |> pull(Fluorophore)
Data <- Luciernaga:::InstrumentReferences(NumberDetectors=54)
Data <- Data |> dplyr::filter(Fluorophore %in% TheFluorophores) |> select(-Instrument) |>
tidyr::pivot_wider(names_from = "Detector", values_from = "AdjustedY")
colnames(Unstained) <- gsub("-A", "", colnames(Unstained))
Unstained <- Unstained |> select(where(is.numeric)) |>
AveragedSignature(stats="median", normalize=TRUE) |>
mutate(Fluorophore="Unstained") |> relocate(Fluorophore, .before=1)
Data <- bind_rows(Data, Unstained)| Fluorophore | UV1 | UV2 | UV3 | UV4 | UV5 | UV6 | UV7 | UV8 | UV9 | UV10 | UV11 | UV12 | UV13 | UV14 | UV15 | UV16 | V1 | V2 | V3 | V4 | V5 | V6 | V7 | V8 | V9 | V10 | V11 | V12 | V13 | V14 | V15 | V16 | B1 | B2 | B3 | B4 | B5 | B6 | B7 | B8 | B9 | B10 | B11 | B12 | B13 | B14 | R1 | R2 | R3 | R4 | R5 | R6 | R7 | R8 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 7-AAD | 0.0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.03 | 0.03 | 0.03 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.38 | 0.26 | 0.24 | 0.19 | 0.13 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.10 | 0.37 | 1.00 | 0.85 | 0.89 | 0.54 | 0.34 | 0.32 | 0.24 | 0.23 | 0.03 | 0.04 | 0.04 | 0.03 | 0.02 | 0.02 | 0.02 | 0.01 |
| Alexa Fluor 700 | 0.0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.18 | 0.13 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.04 | 0.30 | 1.00 | 0.86 | 0.42 | 0.40 | 0.20 |
| APC | 0.0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.20 | 0.06 | 0.06 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.90 | 0.44 | 0.37 | 0.36 | 0.20 | 0.15 | 0.08 |
| APC-Fire 750 | 0.0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.14 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.05 | 0.29 | 1.00 | 0.63 |
| APC-Fire 810 | 0.0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.20 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.05 | 0.05 | 0.04 | 0.04 | 0.03 | 0.04 | 0.31 | 1.00 |
| BV421 | 0.0 | 0.00 | 0.11 | 0.07 | 0.10 | 0.08 | 0.06 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.90 | 0.92 | 0.37 | 0.15 | 0.09 | 0.07 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| BV480 | 0.0 | 0.00 | 0.00 | 0.00 | 0.01 | 0.15 | 0.30 | 0.15 | 0.08 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.20 | 0.91 | 1.00 | 0.80 | 0.76 | 0.32 | 0.18 | 0.16 | 0.04 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.08 | 0.06 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| BV510 | 0.0 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.42 | 0.36 | 0.29 | 0.10 | 0.04 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.10 | 0.25 | 0.70 | 0.70 | 1.00 | 0.66 | 0.44 | 0.42 | 0.15 | 0.07 | 0.06 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| BV570 | 0.0 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.24 | 0.08 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.13 | 0.12 | 0.12 | 0.05 | 0.01 | 0.01 | 0.03 | 1.00 | 0.53 | 0.58 | 0.17 | 0.08 | 0.05 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.05 | 0.04 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| BV605 | 0.0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.21 | 0.11 | 0.05 | 0.04 | 0.03 | 0.02 | 0.01 | 0.05 | 0.05 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.16 | 0.69 | 1.00 | 0.47 | 0.19 | 0.16 | 0.11 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.04 | 0.03 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| BV650 | 0.0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.19 | 0.08 | 0.06 | 0.05 | 0.03 | 0.02 | 0.07 | 0.07 | 0.06 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.20 | 1.00 | 0.46 | 0.37 | 0.22 | 0.13 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.13 | 0.10 | 0.07 | 0.04 | 0.03 | 0.02 | 0.01 |
| BV711 | 0.0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.15 | 0.13 | 0.09 | 0.06 | 0.06 | 0.06 | 0.06 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.29 | 1.00 | 0.64 | 0.46 | 0.20 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.03 | 0.03 | 0.02 | 0.02 | 0.00 | 0.02 | 0.15 | 0.32 | 0.22 | 0.13 | 0.15 | 0.07 |
| BV785 | 0.0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.17 | 0.14 | 0.05 | 0.05 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.23 | 1.00 | 0.56 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.09 | 0.05 |
| FITC | 0.0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.06 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.83 | 1.00 | 0.73 | 0.21 | 0.11 | 0.06 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| Pacific Blue | 0.0 | 0.00 | 0.00 | 0.01 | 0.03 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.58 | 1.00 | 0.66 | 0.33 | 0.18 | 0.15 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| PE | 0.0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.43 | 0.17 | 0.14 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 1.00 | 0.42 | 0.27 | 0.10 | 0.06 | 0.05 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| PE-Cy5 | 0.0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.19 | 0.14 | 0.09 | 0.07 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.85 | 1.00 | 0.72 | 0.33 | 0.23 | 0.18 | 0.11 | 0.10 | 0.23 | 0.41 | 0.28 | 0.17 | 0.14 | 0.08 | 0.07 | 0.03 |
| PE-Cy7 | 0.0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.28 | 0.13 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.44 | 1.00 | 0.86 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.18 | 0.08 |
| PerCP-Cy5.5 | 0.0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.16 | 0.14 | 0.12 | 0.09 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.52 | 0.57 | 0.36 | 0.28 | 0.11 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.57 | 1.00 | 0.60 | 0.32 | 0.32 | 0.25 | 0.21 | 0.01 | 0.18 | 0.36 | 0.33 | 0.19 | 0.14 | 0.16 | 0.06 |
| Spark Blue 550 | 0.0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.33 | 0.19 | 0.13 | 0.11 | 0.04 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.04 | 0.37 | 1.00 | 0.40 | 0.28 | 0.17 | 0.10 | 0.07 | 0.06 | 0.03 | 0.02 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| Unstained | 0.1 | 0.14 | 0.21 | 0.28 | 0.38 | 0.53 | 1.00 | 0.46 | 0.32 | 0.15 | 0.06 | 0.04 | 0.03 | 0.04 | 0.03 | 0.06 | 0.16 | 0.10 | 0.13 | 0.13 | 0.21 | 0.20 | 0.30 | 0.23 | 0.16 | 0.16 | 0.09 | 0.05 | 0.05 | 0.05 | 0.06 | 0.04 | 0.10 | 0.10 | 0.12 | 0.07 | 0.06 | 0.06 | 0.04 | 0.02 | 0.04 | 0.02 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.01 |
[1] "The Complexity Index without the Unstained is 10.39"[1] "The Complexity Index with the Unstained is 10.25"