tests/testthat/_snaps/transformation.md
In JamesHucklesby/vascr: Process Biological Impedance Sensing Data
Can summarise
Code
vascr_summarise(rbgrowth.df, level = "summary")
Output
# A tibble: 312 x 14
Time Unit Frequency Sample Instrument sd totaln n min max
<dbl> <fct> <dbl> <chr> <chr> <dbl> <int> <int> <dbl> <dbl>
1 5 Rb 0 0_cells + ~ ECIS NA 3 1 0 0
2 5 Rb 0 10,000_cel~ ECIS 0 9 3 0 0
3 5 Rb 0 15,000_cel~ ECIS 0 9 3 0 0
4 5 Rb 0 20,000_cel~ ECIS 0 9 3 0 0
5 5 Rb 0 25,000_cel~ ECIS 0 9 3 0 0
6 5 Rb 0 30,000_cel~ ECIS 0 9 3 0 0
7 5 Rb 0 35,000_cel~ ECIS 0 9 3 0 0
8 5 Rb 0 5,000_cell~ ECIS 0.0337 9 3 0 0.06
9 10 Rb 0 0_cells + ~ ECIS NA 3 1 0 0
10 10 Rb 0 10,000_cel~ ECIS 0 9 3 0 0
# i 302 more rows
# i 4 more variables: Well <chr>, Value <dbl>, Experiment <chr>, sem <dbl>
Code
vascr_summarise(rbgrowth.df, level = "experiments")
Output
# A tibble: 858 x 15
Time Unit Frequency Sample Experiment Instrument SampleID Excluded sd
<dbl> <fct> <dbl> <chr> <fct> <chr> <int> <chr> <dbl>
1 5 Rb 0 0_cells ~ 3 : Exper~ ECIS 8 no 0
2 5 Rb 0 10,000_c~ 1 : Exper~ ECIS 6 no 0
3 5 Rb 0 10,000_c~ 2 : Exper~ ECIS 6 no 0
4 5 Rb 0 10,000_c~ 3 : Exper~ ECIS 6 no 0
5 5 Rb 0 15,000_c~ 1 : Exper~ ECIS 5 no 0
6 5 Rb 0 15,000_c~ 2 : Exper~ ECIS 5 no 0
7 5 Rb 0 15,000_c~ 3 : Exper~ ECIS 5 no 0
8 5 Rb 0 20,000_c~ 1 : Exper~ ECIS 4 no 0
9 5 Rb 0 20,000_c~ 2 : Exper~ ECIS 4 no 0
10 5 Rb 0 20,000_c~ 3 : Exper~ ECIS 4 no 0
# i 848 more rows
# i 6 more variables: n <int>, min <dbl>, max <dbl>, Well <chr>, Value <dbl>,
# sem <dbl>
Code
vascr_summarise(rbgrowth.df, level = "experiments") %>% vascr_summarise(level = "summary")
Output
# A tibble: 312 x 14
Time Unit Frequency Sample Instrument sd totaln n min max
<dbl> <fct> <dbl> <chr> <chr> <dbl> <int> <int> <dbl> <dbl>
1 5 Rb 0 0_cells + ~ ECIS NA 3 1 0 0
2 5 Rb 0 10,000_cel~ ECIS 0 9 3 0 0
3 5 Rb 0 15,000_cel~ ECIS 0 9 3 0 0
4 5 Rb 0 20,000_cel~ ECIS 0 9 3 0 0
5 5 Rb 0 25,000_cel~ ECIS 0 9 3 0 0
6 5 Rb 0 30,000_cel~ ECIS 0 9 3 0 0
7 5 Rb 0 35,000_cel~ ECIS 0 9 3 0 0
8 5 Rb 0 5,000_cell~ ECIS 0.0337 9 3 0 0.06
9 10 Rb 0 0_cells + ~ ECIS NA 3 1 0 0
10 10 Rb 0 10,000_cel~ ECIS 0 9 3 0 0
# i 302 more rows
# i 4 more variables: Well <chr>, Value <dbl>, Experiment <chr>, sem <dbl>
Code
vascr_summarise(rbgrowth.df, level = "wells")
Output
# A tibble: 2,574 x 12
Time Unit Well Value Sample Frequency Experiment cells line Instrument
<dbl> <fct> <chr> <dbl> <chr> <dbl> <fct> <chr> <chr> <chr>
1 5 Rb A01 0 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
2 5 Rb A02 0 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
3 5 Rb A03 0 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
4 5 Rb B01 0 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
5 5 Rb B02 0 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
6 5 Rb B03 0 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
7 5 Rb C01 0 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
8 5 Rb C02 0 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
9 5 Rb C03 0 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
10 5 Rb D01 0 20,000_c~ 0 1 : Exper~ 20000 HCME~ ECIS
# i 2,564 more rows
# i 2 more variables: SampleID <int>, Excluded <chr>
Code
vascr_summarise(rbgrowth.df, level = "median_deviation")
Output
# A tibble: 2,574 x 15
# Groups: Time, Experiment, SampleID, Excluded [858]
Time Unit Well Value Sample Frequency Experiment cells line Instrument
<dbl> <fct> <chr> <dbl> <chr> <dbl> <fct> <chr> <chr> <chr>
1 5 Rb A01 0 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
2 5 Rb A02 0 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
3 5 Rb A03 0 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
4 5 Rb B01 0 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
5 5 Rb B02 0 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
6 5 Rb B03 0 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
7 5 Rb C01 0 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
8 5 Rb C02 0 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
9 5 Rb C03 0 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
10 5 Rb D01 0 20,000_c~ 0 1 : Exper~ 20000 HCME~ ECIS
# i 2,564 more rows
# i 5 more variables: SampleID <int>, Excluded <chr>, Median_Deviation <dbl>,
# Median_Value <dbl>, MAD <dbl>
Requested data is less summarised than the data input, try again
Code
vascr_summarise_summary(vascr_summarise(rbgrowth.df, "summary"))
Output
# A tibble: 312 x 14
Time Unit Frequency Sample Instrument sd totaln n min max
<dbl> <fct> <dbl> <chr> <chr> <dbl> <int> <int> <dbl> <dbl>
1 5 Rb 0 0_cells + ~ ECIS NA 3 1 0 0
2 5 Rb 0 10,000_cel~ ECIS 0 9 3 0 0
3 5 Rb 0 15,000_cel~ ECIS 0 9 3 0 0
4 5 Rb 0 20,000_cel~ ECIS 0 9 3 0 0
5 5 Rb 0 25,000_cel~ ECIS 0 9 3 0 0
6 5 Rb 0 30,000_cel~ ECIS 0 9 3 0 0
7 5 Rb 0 35,000_cel~ ECIS 0 9 3 0 0
8 5 Rb 0 5,000_cell~ ECIS 0.0337 9 3 0 0.06
9 10 Rb 0 0_cells + ~ ECIS NA 3 1 0 0
10 10 Rb 0 10,000_cel~ ECIS 0 9 3 0 0
# i 302 more rows
# i 4 more variables: Well <chr>, Value <dbl>, Experiment <chr>, sem <dbl>
Code
w16 = system.file("extdata/instruments/ecis_16_testplate.abp", package = "vascr")
d16 = vascr_import("ECIS", raw = w16, experiment = "W16")
Code
vascr_check_resampled(d16)
Output
[1] FALSE
Code
vascr_summarise(d16 %>% vascr_subset(unit = "R", frequency = 4000), "summary")
Output
# A tibble: 2 x 14
Time Unit Frequency Sample Instrument sd totaln n min max Well
<dbl> <fct> <dbl> <chr> <chr> <dbl> <int> <int> <dbl> <dbl> <chr>
1 6.88e-4 R 4000 NA ECIS NA 8 1 4504. 4504. A01,~
2 6.73e-2 R 4000 NA ECIS NA 8 1 4503. 4503. A01,~
# i 3 more variables: Value <dbl>, Experiment <chr>, sem <dbl>
Can summarise deviation
Code
vascr_summarise(growth.df %>% vascr_subset(unit = "R", frequency = "4000"),
level = "median_deviation")
Output
# A tibble: 2,808 x 15
# Groups: Time, Experiment, SampleID, Excluded [936]
Time Unit Well Value Sample Frequency Experiment cells line Instrument
<dbl> <fct> <chr> <dbl> <chr> <dbl> <fct> <chr> <chr> <chr>
1 5 R A01 302. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
2 10 R A01 342. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
3 15 R A01 405. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
4 20 R A01 469. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
5 25 R A01 514. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
6 30 R A01 535. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
7 35 R A01 572. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
8 40 R A01 620. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
9 45 R A01 664. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
10 50 R A01 690. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
# i 2,798 more rows
# i 5 more variables: SampleID <int>, Excluded <chr>, Median_Deviation <dbl>,
# Median_Value <dbl>, MAD <dbl>
Can normalise
Code
vascr_normalise(data.df = rgrowth.df, 100)
Output
# A tibble: 1,440 x 10
Time Unit Value Well Sample Frequency Experiment Instrument SampleID
<dbl> <fct> <dbl> <chr> <chr> <dbl> <fct> <chr> <int>
1 5 R -298. A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
2 10 R -257. A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
3 15 R -194. A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
4 20 R -130. A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
5 25 R -84.8 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
6 30 R -63.9 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
7 35 R -27.0 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
8 40 R 21.3 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
9 45 R 65.3 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
10 50 R 90.6 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
# i 1,430 more rows
# i 1 more variable: Excluded <chr>
Code
vascr_normalise(rgrowth.df, 100, divide = TRUE)
Output
# A tibble: 1,440 x 10
Time Unit Value Well Sample Frequency Experiment Instrument SampleID
<dbl> <fct> <dbl> <chr> <chr> <dbl> <fct> <chr> <int>
1 5 R 0.503 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
2 10 R 0.570 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
3 15 R 0.677 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
4 20 R 0.783 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
5 25 R 0.858 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
6 30 R 0.893 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
7 35 R 0.955 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
8 40 R 1.04 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
9 45 R 1.11 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
10 50 R 1.15 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
# i 1,430 more rows
# i 1 more variable: Excluded <chr>
Code
vascr_normalise(rgrowth.df, 100)
Output
# A tibble: 2,808 x 10
Time Unit Value Well Sample Frequency Experiment Instrument SampleID
<dbl> <fct> <dbl> <chr> <chr> <dbl> <fct> <chr> <int>
1 5 R -298. A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
2 10 R -257. A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
3 15 R -194. A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
4 20 R -130. A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
5 25 R -84.8 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
6 30 R -63.9 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
7 35 R -27.0 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
8 40 R 21.3 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
9 45 R 65.3 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
10 50 R 90.6 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
# i 2,798 more rows
# i 1 more variable: Excluded <chr>
Code
vascr_normalise(growth.df, NULL)
Output
# A tibble: 146,370 x 12
Time Unit Well Value Sample Frequency Experiment cells line Instrument
<dbl> <chr> <chr> <dbl> <chr> <dbl> <fct> <chr> <chr> <chr>
1 0 Alpha A01 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
2 0 Alpha A02 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
3 0 Alpha A03 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
4 0 Alpha B01 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
5 0 Alpha B02 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
6 0 Alpha B03 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
7 0 Alpha C01 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
8 0 Alpha C02 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
9 0 Alpha C03 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
10 0 Alpha D01 NA 20,000_c~ 0 1 : Exper~ 20000 HCME~ ECIS
# i 146,360 more rows
# i 2 more variables: SampleID <int>, Excluded <chr>
Can subsample
Code
vascr_subsample(growth.df, 10)
Output
# A tibble: 17,850 x 12
Time Unit Well Value Sample Frequency Experiment cells line Instrument
<dbl> <chr> <chr> <dbl> <chr> <dbl> <fct> <chr> <chr> <chr>
1 0 Alpha A01 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
2 0 Alpha A02 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
3 0 Alpha A03 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
4 0 Alpha B01 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
5 0 Alpha B02 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
6 0 Alpha B03 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
7 0 Alpha C01 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
8 0 Alpha C02 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
9 0 Alpha C03 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
10 0 Alpha D01 NA 20,000_c~ 0 1 : Exper~ 20000 HCME~ ECIS
# i 17,840 more rows
# i 2 more variables: SampleID <int>, Excluded <chr>
Code
vascr_subsample(growth.df, Inf)
Output
# A tibble: 146,370 x 12
Time Unit Well Value Sample Frequency Experiment cells line Instrument
<dbl> <chr> <chr> <dbl> <chr> <dbl> <fct> <chr> <chr> <chr>
1 0 Alpha A01 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
2 0 Alpha A02 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
3 0 Alpha A03 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
4 0 Alpha B01 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
5 0 Alpha B02 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
6 0 Alpha B03 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
7 0 Alpha C01 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
8 0 Alpha C02 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
9 0 Alpha C03 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
10 0 Alpha D01 NA 20,000_c~ 0 1 : Exper~ 20000 HCME~ ECIS
# i 146,360 more rows
# i 2 more variables: SampleID <int>, Excluded <chr>
Code
vascr_subsample(growth.df %>% vascr_subset(time = 10), 10)
Output
# A tibble: 3,570 x 12
Time Unit Well Value Sample Frequency Experiment cells line Instrument
<dbl> <chr> <chr> <dbl> <chr> <dbl> <fct> <chr> <chr> <chr>
1 10 Alpha A01 3.34 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
2 10 Alpha A02 3.77 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
3 10 Alpha A03 3.25 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
4 10 Alpha B01 3.15 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
5 10 Alpha B02 3.4 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
6 10 Alpha B03 2.89 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
7 10 Alpha C01 2.71 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
8 10 Alpha C02 2.88 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
9 10 Alpha C03 2.83 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
10 10 Alpha D01 2.27 20,000_c~ 0 1 : Exper~ 20000 HCME~ ECIS
# i 3,560 more rows
# i 2 more variables: SampleID <int>, Excluded <chr>
Code
vascr_resample_time(growth.df, t_start = 5, t_end = 20, rate = 5)
Output
# A tibble: 14,280 x 12
Unit Well Sample Frequency Experiment cells line Instrument SampleID
<chr> <chr> <chr> <dbl> <fct> <chr> <chr> <chr> <int>
1 Alpha A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
2 Alpha A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
3 Alpha A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
4 Alpha A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
5 Alpha A02 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
6 Alpha A02 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
7 Alpha A02 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
8 Alpha A02 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
9 Alpha A03 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
10 Alpha A03 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
# i 14,270 more rows
# i 3 more variables: Excluded <chr>, Value <dbl>, Time <dbl>
Can interpolate time
Code
vascr_interpolate_time(growth.df %>% vascr_subset(unit = "Rb"))
Output
# A tibble: 2,574 x 12
Unit Well Sample Frequency Experiment cells line Instrument SampleID
<fct> <chr> <chr> <dbl> <fct> <chr> <chr> <chr> <int>
1 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
2 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
3 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
4 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
5 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
6 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
7 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
8 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
9 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
10 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
# i 2,564 more rows
# i 3 more variables: Excluded <chr>, Value <dbl>, Time <dbl>
vascr_interpolate_time only supports one unit and frequency at a time
Can interpolate time unresampled dataset
Code
vascr_resample_time(growth_unresampled.df %>% vascr_subset(unit = "R",
frequency = 4000))
Output
# A tibble: 8,100 x 10
Unit Well Frequency Instrument Experiment Sample SampleID Excluded Value
<fct> <chr> <dbl> <chr> <fct> <chr> <dbl> <lgl> <dbl>
1 R A01 4000 ECIS "1 : " A01 1 FALSE 276.
2 R A01 4000 ECIS "1 : " A01 1 FALSE 276.
3 R A01 4000 ECIS "1 : " A01 1 FALSE 277.
4 R A01 4000 ECIS "1 : " A01 1 FALSE 278.
5 R A01 4000 ECIS "1 : " A01 1 FALSE 279.
6 R A01 4000 ECIS "1 : " A01 1 FALSE 280.
7 R A01 4000 ECIS "1 : " A01 1 FALSE 281.
8 R A01 4000 ECIS "1 : " A01 1 FALSE 281.
9 R A01 4000 ECIS "1 : " A01 1 FALSE 282.
10 R A01 4000 ECIS "1 : " A01 1 FALSE 283.
# i 8,090 more rows
# i 1 more variable: Time <dbl>
vascr_force_resampled
Code
vascr_force_resampled(growth.df)
Output
# A tibble: 146,370 x 12
Time Unit Well Value Sample Frequency Experiment cells line Instrument
<dbl> <chr> <chr> <dbl> <chr> <dbl> <fct> <chr> <chr> <chr>
1 0 Alpha A01 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
2 0 Alpha A02 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
3 0 Alpha A03 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
4 0 Alpha B01 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
5 0 Alpha B02 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
6 0 Alpha B03 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
7 0 Alpha C01 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
8 0 Alpha C02 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
9 0 Alpha C03 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
10 0 Alpha D01 NA 20,000_c~ 0 1 : Exper~ 20000 HCME~ ECIS
# i 146,360 more rows
# i 2 more variables: SampleID <int>, Excluded <chr>
Code
vascr_force_resampled(growth_unresampled.df)
Message
! Data is not resampled, resampling to allow further analytics
Output
# A tibble: 48,600 x 10
Unit Well Frequency Instrument Experiment Sample SampleID Excluded Value
<fct> <chr> <dbl> <chr> <fct> <chr> <dbl> <chr> <dbl>
1 R A01 1000 ECIS "1 : " A01 1 no 383.
2 R A01 1000 ECIS "1 : " A01 1 no 383.
3 R A01 1000 ECIS "1 : " A01 1 no 385.
4 R A01 1000 ECIS "1 : " A01 1 no 386.
5 R A01 1000 ECIS "1 : " A01 1 no 387.
6 R A01 1000 ECIS "1 : " A01 1 no 388.
7 R A01 1000 ECIS "1 : " A01 1 no 389.
8 R A01 1000 ECIS "1 : " A01 1 no 389.
9 R A01 1000 ECIS "1 : " A01 1 no 390.
10 R A01 1000 ECIS "1 : " A01 1 no 391.
# i 48,590 more rows
# i 1 more variable: Time <dbl>
vascr time samples counts correctly
Code
vascr_find_count_timepoints(growth.df)
Output
[1] 41
vascr AUC works
Code
vascr_auc(growth.df %>% vascr_subset(experiment = 1, well = "A01", unit = "R",
frequency = 4000))
Output
[1] 101819.7
plot of resample degradation works
Code
p1 = vascr_plot_resample_range(data.df = growth.df)
Message
i Recomended resampling rate: 29
remove metadata
Code
growth.df %>% vascr_remove_metadata()
Output
# A tibble: 146,370 x 10
Time Unit Value Well Sample Frequency Experiment Instrument SampleID
<dbl> <chr> <dbl> <chr> <chr> <dbl> <fct> <chr> <int>
1 0 Alpha NA A01 35,000_cell~ 0 1 : Exper~ ECIS 1
2 0 Alpha NA A02 35,000_cell~ 0 1 : Exper~ ECIS 1
3 0 Alpha NA A03 35,000_cell~ 0 1 : Exper~ ECIS 1
4 0 Alpha NA B01 30,000_cell~ 0 1 : Exper~ ECIS 2
5 0 Alpha NA B02 30,000_cell~ 0 1 : Exper~ ECIS 2
6 0 Alpha NA B03 30,000_cell~ 0 1 : Exper~ ECIS 2
7 0 Alpha NA C01 25,000_cell~ 0 1 : Exper~ ECIS 3
8 0 Alpha NA C02 25,000_cell~ 0 1 : Exper~ ECIS 3
9 0 Alpha NA C03 25,000_cell~ 0 1 : Exper~ ECIS 3
10 0 Alpha NA D01 20,000_cell~ 0 1 : Exper~ ECIS 4
# i 146,360 more rows
# i 1 more variable: Excluded <chr>
Code
vascr_summarise(growth.df %>% vascr_subset(unit = "R", frequency = 4000),
"experiments") %>% vascr_remove_metadata()
Message
! You are removing some summary statistics. These are not re-generatable using vascr_explode alone, and must be regenerated with vascr_summarise.
Output
# A tibble: 936 x 10
Time Unit Value Well Sample Frequency Experiment Instrument SampleID
<dbl> <fct> <dbl> <chr> <chr> <dbl> <fct> <chr> <int>
1 5 R 241. H01,H02,H03 0_cel~ 4000 1 : Exper~ ECIS 8
2 5 R 247. H04,H05,H06 0_cel~ 4000 2 : Exper~ ECIS 8
3 5 R 247. H07,H08,H09 0_cel~ 4000 3 : Exper~ ECIS 8
4 5 R 256. F01,F02,F03 10,00~ 4000 1 : Exper~ ECIS 6
5 5 R 267. F04,F05,F06 10,00~ 4000 2 : Exper~ ECIS 6
6 5 R 265. F07,F08,F09 10,00~ 4000 3 : Exper~ ECIS 6
7 5 R 263. E01,E02,E03 15,00~ 4000 1 : Exper~ ECIS 5
8 5 R 280. E04,E05,E06 15,00~ 4000 2 : Exper~ ECIS 5
9 5 R 273. E07,E08,E09 15,00~ 4000 3 : Exper~ ECIS 5
10 5 R 272. D01,D02,D03 20,00~ 4000 1 : Exper~ ECIS 4
# i 926 more rows
# i 1 more variable: Excluded <chr>
JamesHucklesby/vascr documentation built on July 16, 2025, 8:16 p.m.
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Can summarise
Code
vascr_summarise(rbgrowth.df, level = "summary")
Output
# A tibble: 312 x 14
Time Unit Frequency Sample Instrument sd totaln n min max
<dbl> <fct> <dbl> <chr> <chr> <dbl> <int> <int> <dbl> <dbl>
1 5 Rb 0 0_cells + ~ ECIS NA 3 1 0 0
2 5 Rb 0 10,000_cel~ ECIS 0 9 3 0 0
3 5 Rb 0 15,000_cel~ ECIS 0 9 3 0 0
4 5 Rb 0 20,000_cel~ ECIS 0 9 3 0 0
5 5 Rb 0 25,000_cel~ ECIS 0 9 3 0 0
6 5 Rb 0 30,000_cel~ ECIS 0 9 3 0 0
7 5 Rb 0 35,000_cel~ ECIS 0 9 3 0 0
8 5 Rb 0 5,000_cell~ ECIS 0.0337 9 3 0 0.06
9 10 Rb 0 0_cells + ~ ECIS NA 3 1 0 0
10 10 Rb 0 10,000_cel~ ECIS 0 9 3 0 0
# i 302 more rows
# i 4 more variables: Well <chr>, Value <dbl>, Experiment <chr>, sem <dbl>
Code
vascr_summarise(rbgrowth.df, level = "experiments")
Output
# A tibble: 858 x 15
Time Unit Frequency Sample Experiment Instrument SampleID Excluded sd
<dbl> <fct> <dbl> <chr> <fct> <chr> <int> <chr> <dbl>
1 5 Rb 0 0_cells ~ 3 : Exper~ ECIS 8 no 0
2 5 Rb 0 10,000_c~ 1 : Exper~ ECIS 6 no 0
3 5 Rb 0 10,000_c~ 2 : Exper~ ECIS 6 no 0
4 5 Rb 0 10,000_c~ 3 : Exper~ ECIS 6 no 0
5 5 Rb 0 15,000_c~ 1 : Exper~ ECIS 5 no 0
6 5 Rb 0 15,000_c~ 2 : Exper~ ECIS 5 no 0
7 5 Rb 0 15,000_c~ 3 : Exper~ ECIS 5 no 0
8 5 Rb 0 20,000_c~ 1 : Exper~ ECIS 4 no 0
9 5 Rb 0 20,000_c~ 2 : Exper~ ECIS 4 no 0
10 5 Rb 0 20,000_c~ 3 : Exper~ ECIS 4 no 0
# i 848 more rows
# i 6 more variables: n <int>, min <dbl>, max <dbl>, Well <chr>, Value <dbl>,
# sem <dbl>
Code
vascr_summarise(rbgrowth.df, level = "experiments") %>% vascr_summarise(level = "summary")
Output
# A tibble: 312 x 14
Time Unit Frequency Sample Instrument sd totaln n min max
<dbl> <fct> <dbl> <chr> <chr> <dbl> <int> <int> <dbl> <dbl>
1 5 Rb 0 0_cells + ~ ECIS NA 3 1 0 0
2 5 Rb 0 10,000_cel~ ECIS 0 9 3 0 0
3 5 Rb 0 15,000_cel~ ECIS 0 9 3 0 0
4 5 Rb 0 20,000_cel~ ECIS 0 9 3 0 0
5 5 Rb 0 25,000_cel~ ECIS 0 9 3 0 0
6 5 Rb 0 30,000_cel~ ECIS 0 9 3 0 0
7 5 Rb 0 35,000_cel~ ECIS 0 9 3 0 0
8 5 Rb 0 5,000_cell~ ECIS 0.0337 9 3 0 0.06
9 10 Rb 0 0_cells + ~ ECIS NA 3 1 0 0
10 10 Rb 0 10,000_cel~ ECIS 0 9 3 0 0
# i 302 more rows
# i 4 more variables: Well <chr>, Value <dbl>, Experiment <chr>, sem <dbl>
Code
vascr_summarise(rbgrowth.df, level = "wells")
Output
# A tibble: 2,574 x 12
Time Unit Well Value Sample Frequency Experiment cells line Instrument
<dbl> <fct> <chr> <dbl> <chr> <dbl> <fct> <chr> <chr> <chr>
1 5 Rb A01 0 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
2 5 Rb A02 0 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
3 5 Rb A03 0 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
4 5 Rb B01 0 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
5 5 Rb B02 0 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
6 5 Rb B03 0 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
7 5 Rb C01 0 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
8 5 Rb C02 0 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
9 5 Rb C03 0 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
10 5 Rb D01 0 20,000_c~ 0 1 : Exper~ 20000 HCME~ ECIS
# i 2,564 more rows
# i 2 more variables: SampleID <int>, Excluded <chr>
Code
vascr_summarise(rbgrowth.df, level = "median_deviation")
Output
# A tibble: 2,574 x 15
# Groups: Time, Experiment, SampleID, Excluded [858]
Time Unit Well Value Sample Frequency Experiment cells line Instrument
<dbl> <fct> <chr> <dbl> <chr> <dbl> <fct> <chr> <chr> <chr>
1 5 Rb A01 0 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
2 5 Rb A02 0 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
3 5 Rb A03 0 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
4 5 Rb B01 0 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
5 5 Rb B02 0 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
6 5 Rb B03 0 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
7 5 Rb C01 0 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
8 5 Rb C02 0 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
9 5 Rb C03 0 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
10 5 Rb D01 0 20,000_c~ 0 1 : Exper~ 20000 HCME~ ECIS
# i 2,564 more rows
# i 5 more variables: SampleID <int>, Excluded <chr>, Median_Deviation <dbl>,
# Median_Value <dbl>, MAD <dbl>
Requested data is less summarised than the data input, try again
Code
vascr_summarise_summary(vascr_summarise(rbgrowth.df, "summary"))
Output
# A tibble: 312 x 14
Time Unit Frequency Sample Instrument sd totaln n min max
<dbl> <fct> <dbl> <chr> <chr> <dbl> <int> <int> <dbl> <dbl>
1 5 Rb 0 0_cells + ~ ECIS NA 3 1 0 0
2 5 Rb 0 10,000_cel~ ECIS 0 9 3 0 0
3 5 Rb 0 15,000_cel~ ECIS 0 9 3 0 0
4 5 Rb 0 20,000_cel~ ECIS 0 9 3 0 0
5 5 Rb 0 25,000_cel~ ECIS 0 9 3 0 0
6 5 Rb 0 30,000_cel~ ECIS 0 9 3 0 0
7 5 Rb 0 35,000_cel~ ECIS 0 9 3 0 0
8 5 Rb 0 5,000_cell~ ECIS 0.0337 9 3 0 0.06
9 10 Rb 0 0_cells + ~ ECIS NA 3 1 0 0
10 10 Rb 0 10,000_cel~ ECIS 0 9 3 0 0
# i 302 more rows
# i 4 more variables: Well <chr>, Value <dbl>, Experiment <chr>, sem <dbl>
Code
w16 = system.file("extdata/instruments/ecis_16_testplate.abp", package = "vascr")
d16 = vascr_import("ECIS", raw = w16, experiment = "W16")
Code
vascr_check_resampled(d16)
Output
[1] FALSE
Code
vascr_summarise(d16 %>% vascr_subset(unit = "R", frequency = 4000), "summary")
Output
# A tibble: 2 x 14
Time Unit Frequency Sample Instrument sd totaln n min max Well
<dbl> <fct> <dbl> <chr> <chr> <dbl> <int> <int> <dbl> <dbl> <chr>
1 6.88e-4 R 4000 NA ECIS NA 8 1 4504. 4504. A01,~
2 6.73e-2 R 4000 NA ECIS NA 8 1 4503. 4503. A01,~
# i 3 more variables: Value <dbl>, Experiment <chr>, sem <dbl>
Can summarise deviation
Code
vascr_summarise(growth.df %>% vascr_subset(unit = "R", frequency = "4000"),
level = "median_deviation")
Output
# A tibble: 2,808 x 15
# Groups: Time, Experiment, SampleID, Excluded [936]
Time Unit Well Value Sample Frequency Experiment cells line Instrument
<dbl> <fct> <chr> <dbl> <chr> <dbl> <fct> <chr> <chr> <chr>
1 5 R A01 302. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
2 10 R A01 342. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
3 15 R A01 405. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
4 20 R A01 469. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
5 25 R A01 514. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
6 30 R A01 535. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
7 35 R A01 572. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
8 40 R A01 620. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
9 45 R A01 664. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
10 50 R A01 690. 35,000_c~ 4000 1 : Exper~ 35000 HCME~ ECIS
# i 2,798 more rows
# i 5 more variables: SampleID <int>, Excluded <chr>, Median_Deviation <dbl>,
# Median_Value <dbl>, MAD <dbl>
Can normalise
Code
vascr_normalise(data.df = rgrowth.df, 100)
Output
# A tibble: 1,440 x 10
Time Unit Value Well Sample Frequency Experiment Instrument SampleID
<dbl> <fct> <dbl> <chr> <chr> <dbl> <fct> <chr> <int>
1 5 R -298. A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
2 10 R -257. A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
3 15 R -194. A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
4 20 R -130. A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
5 25 R -84.8 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
6 30 R -63.9 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
7 35 R -27.0 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
8 40 R 21.3 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
9 45 R 65.3 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
10 50 R 90.6 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
# i 1,430 more rows
# i 1 more variable: Excluded <chr>
Code
vascr_normalise(rgrowth.df, 100, divide = TRUE)
Output
# A tibble: 1,440 x 10
Time Unit Value Well Sample Frequency Experiment Instrument SampleID
<dbl> <fct> <dbl> <chr> <chr> <dbl> <fct> <chr> <int>
1 5 R 0.503 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
2 10 R 0.570 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
3 15 R 0.677 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
4 20 R 0.783 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
5 25 R 0.858 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
6 30 R 0.893 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
7 35 R 0.955 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
8 40 R 1.04 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
9 45 R 1.11 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
10 50 R 1.15 A01 35,000_cell~ 4000 1 : Exper~ ECIS 1
# i 1,430 more rows
# i 1 more variable: Excluded <chr>
Code
vascr_normalise(rgrowth.df, 100)
Output
# A tibble: 2,808 x 10
Time Unit Value Well Sample Frequency Experiment Instrument SampleID
<dbl> <fct> <dbl> <chr> <chr> <dbl> <fct> <chr> <int>
1 5 R -298. A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
2 10 R -257. A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
3 15 R -194. A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
4 20 R -130. A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
5 25 R -84.8 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
6 30 R -63.9 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
7 35 R -27.0 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
8 40 R 21.3 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
9 45 R 65.3 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
10 50 R 90.6 A01 35,000_cel~ 4000 1 : Exper~ ECIS 1
# i 2,798 more rows
# i 1 more variable: Excluded <chr>
Code
vascr_normalise(growth.df, NULL)
Output
# A tibble: 146,370 x 12
Time Unit Well Value Sample Frequency Experiment cells line Instrument
<dbl> <chr> <chr> <dbl> <chr> <dbl> <fct> <chr> <chr> <chr>
1 0 Alpha A01 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
2 0 Alpha A02 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
3 0 Alpha A03 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
4 0 Alpha B01 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
5 0 Alpha B02 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
6 0 Alpha B03 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
7 0 Alpha C01 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
8 0 Alpha C02 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
9 0 Alpha C03 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
10 0 Alpha D01 NA 20,000_c~ 0 1 : Exper~ 20000 HCME~ ECIS
# i 146,360 more rows
# i 2 more variables: SampleID <int>, Excluded <chr>
Can subsample
Code
vascr_subsample(growth.df, 10)
Output
# A tibble: 17,850 x 12
Time Unit Well Value Sample Frequency Experiment cells line Instrument
<dbl> <chr> <chr> <dbl> <chr> <dbl> <fct> <chr> <chr> <chr>
1 0 Alpha A01 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
2 0 Alpha A02 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
3 0 Alpha A03 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
4 0 Alpha B01 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
5 0 Alpha B02 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
6 0 Alpha B03 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
7 0 Alpha C01 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
8 0 Alpha C02 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
9 0 Alpha C03 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
10 0 Alpha D01 NA 20,000_c~ 0 1 : Exper~ 20000 HCME~ ECIS
# i 17,840 more rows
# i 2 more variables: SampleID <int>, Excluded <chr>
Code
vascr_subsample(growth.df, Inf)
Output
# A tibble: 146,370 x 12
Time Unit Well Value Sample Frequency Experiment cells line Instrument
<dbl> <chr> <chr> <dbl> <chr> <dbl> <fct> <chr> <chr> <chr>
1 0 Alpha A01 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
2 0 Alpha A02 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
3 0 Alpha A03 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
4 0 Alpha B01 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
5 0 Alpha B02 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
6 0 Alpha B03 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
7 0 Alpha C01 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
8 0 Alpha C02 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
9 0 Alpha C03 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
10 0 Alpha D01 NA 20,000_c~ 0 1 : Exper~ 20000 HCME~ ECIS
# i 146,360 more rows
# i 2 more variables: SampleID <int>, Excluded <chr>
Code
vascr_subsample(growth.df %>% vascr_subset(time = 10), 10)
Output
# A tibble: 3,570 x 12
Time Unit Well Value Sample Frequency Experiment cells line Instrument
<dbl> <chr> <chr> <dbl> <chr> <dbl> <fct> <chr> <chr> <chr>
1 10 Alpha A01 3.34 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
2 10 Alpha A02 3.77 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
3 10 Alpha A03 3.25 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
4 10 Alpha B01 3.15 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
5 10 Alpha B02 3.4 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
6 10 Alpha B03 2.89 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
7 10 Alpha C01 2.71 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
8 10 Alpha C02 2.88 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
9 10 Alpha C03 2.83 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
10 10 Alpha D01 2.27 20,000_c~ 0 1 : Exper~ 20000 HCME~ ECIS
# i 3,560 more rows
# i 2 more variables: SampleID <int>, Excluded <chr>
Code
vascr_resample_time(growth.df, t_start = 5, t_end = 20, rate = 5)
Output
# A tibble: 14,280 x 12
Unit Well Sample Frequency Experiment cells line Instrument SampleID
<chr> <chr> <chr> <dbl> <fct> <chr> <chr> <chr> <int>
1 Alpha A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
2 Alpha A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
3 Alpha A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
4 Alpha A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
5 Alpha A02 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
6 Alpha A02 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
7 Alpha A02 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
8 Alpha A02 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
9 Alpha A03 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
10 Alpha A03 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
# i 14,270 more rows
# i 3 more variables: Excluded <chr>, Value <dbl>, Time <dbl>
Can interpolate time
Code
vascr_interpolate_time(growth.df %>% vascr_subset(unit = "Rb"))
Output
# A tibble: 2,574 x 12
Unit Well Sample Frequency Experiment cells line Instrument SampleID
<fct> <chr> <chr> <dbl> <fct> <chr> <chr> <chr> <int>
1 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
2 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
3 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
4 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
5 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
6 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
7 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
8 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
9 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
10 Rb A01 35,000_cell~ 0 1 : Exper~ 35000 HCME~ ECIS 1
# i 2,564 more rows
# i 3 more variables: Excluded <chr>, Value <dbl>, Time <dbl>
vascr_interpolate_time only supports one unit and frequency at a time
Can interpolate time unresampled dataset
Code
vascr_resample_time(growth_unresampled.df %>% vascr_subset(unit = "R",
frequency = 4000))
Output
# A tibble: 8,100 x 10
Unit Well Frequency Instrument Experiment Sample SampleID Excluded Value
<fct> <chr> <dbl> <chr> <fct> <chr> <dbl> <lgl> <dbl>
1 R A01 4000 ECIS "1 : " A01 1 FALSE 276.
2 R A01 4000 ECIS "1 : " A01 1 FALSE 276.
3 R A01 4000 ECIS "1 : " A01 1 FALSE 277.
4 R A01 4000 ECIS "1 : " A01 1 FALSE 278.
5 R A01 4000 ECIS "1 : " A01 1 FALSE 279.
6 R A01 4000 ECIS "1 : " A01 1 FALSE 280.
7 R A01 4000 ECIS "1 : " A01 1 FALSE 281.
8 R A01 4000 ECIS "1 : " A01 1 FALSE 281.
9 R A01 4000 ECIS "1 : " A01 1 FALSE 282.
10 R A01 4000 ECIS "1 : " A01 1 FALSE 283.
# i 8,090 more rows
# i 1 more variable: Time <dbl>
vascr_force_resampled
Code
vascr_force_resampled(growth.df)
Output
# A tibble: 146,370 x 12
Time Unit Well Value Sample Frequency Experiment cells line Instrument
<dbl> <chr> <chr> <dbl> <chr> <dbl> <fct> <chr> <chr> <chr>
1 0 Alpha A01 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
2 0 Alpha A02 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
3 0 Alpha A03 NA 35,000_c~ 0 1 : Exper~ 35000 HCME~ ECIS
4 0 Alpha B01 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
5 0 Alpha B02 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
6 0 Alpha B03 NA 30,000_c~ 0 1 : Exper~ 30000 HCME~ ECIS
7 0 Alpha C01 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
8 0 Alpha C02 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
9 0 Alpha C03 NA 25,000_c~ 0 1 : Exper~ 25000 HCME~ ECIS
10 0 Alpha D01 NA 20,000_c~ 0 1 : Exper~ 20000 HCME~ ECIS
# i 146,360 more rows
# i 2 more variables: SampleID <int>, Excluded <chr>
Code
vascr_force_resampled(growth_unresampled.df)
Message
! Data is not resampled, resampling to allow further analytics
Output
# A tibble: 48,600 x 10
Unit Well Frequency Instrument Experiment Sample SampleID Excluded Value
<fct> <chr> <dbl> <chr> <fct> <chr> <dbl> <chr> <dbl>
1 R A01 1000 ECIS "1 : " A01 1 no 383.
2 R A01 1000 ECIS "1 : " A01 1 no 383.
3 R A01 1000 ECIS "1 : " A01 1 no 385.
4 R A01 1000 ECIS "1 : " A01 1 no 386.
5 R A01 1000 ECIS "1 : " A01 1 no 387.
6 R A01 1000 ECIS "1 : " A01 1 no 388.
7 R A01 1000 ECIS "1 : " A01 1 no 389.
8 R A01 1000 ECIS "1 : " A01 1 no 389.
9 R A01 1000 ECIS "1 : " A01 1 no 390.
10 R A01 1000 ECIS "1 : " A01 1 no 391.
# i 48,590 more rows
# i 1 more variable: Time <dbl>
vascr time samples counts correctly
Code
vascr_find_count_timepoints(growth.df)
Output
[1] 41
vascr AUC works
Code
vascr_auc(growth.df %>% vascr_subset(experiment = 1, well = "A01", unit = "R",
frequency = 4000))
Output
[1] 101819.7
plot of resample degradation works
Code
p1 = vascr_plot_resample_range(data.df = growth.df)
Message
i Recomended resampling rate: 29
remove metadata
Code
growth.df %>% vascr_remove_metadata()
Output
# A tibble: 146,370 x 10
Time Unit Value Well Sample Frequency Experiment Instrument SampleID
<dbl> <chr> <dbl> <chr> <chr> <dbl> <fct> <chr> <int>
1 0 Alpha NA A01 35,000_cell~ 0 1 : Exper~ ECIS 1
2 0 Alpha NA A02 35,000_cell~ 0 1 : Exper~ ECIS 1
3 0 Alpha NA A03 35,000_cell~ 0 1 : Exper~ ECIS 1
4 0 Alpha NA B01 30,000_cell~ 0 1 : Exper~ ECIS 2
5 0 Alpha NA B02 30,000_cell~ 0 1 : Exper~ ECIS 2
6 0 Alpha NA B03 30,000_cell~ 0 1 : Exper~ ECIS 2
7 0 Alpha NA C01 25,000_cell~ 0 1 : Exper~ ECIS 3
8 0 Alpha NA C02 25,000_cell~ 0 1 : Exper~ ECIS 3
9 0 Alpha NA C03 25,000_cell~ 0 1 : Exper~ ECIS 3
10 0 Alpha NA D01 20,000_cell~ 0 1 : Exper~ ECIS 4
# i 146,360 more rows
# i 1 more variable: Excluded <chr>
Code
vascr_summarise(growth.df %>% vascr_subset(unit = "R", frequency = 4000),
"experiments") %>% vascr_remove_metadata()
Message
! You are removing some summary statistics. These are not re-generatable using vascr_explode alone, and must be regenerated with vascr_summarise.
Output
# A tibble: 936 x 10
Time Unit Value Well Sample Frequency Experiment Instrument SampleID
<dbl> <fct> <dbl> <chr> <chr> <dbl> <fct> <chr> <int>
1 5 R 241. H01,H02,H03 0_cel~ 4000 1 : Exper~ ECIS 8
2 5 R 247. H04,H05,H06 0_cel~ 4000 2 : Exper~ ECIS 8
3 5 R 247. H07,H08,H09 0_cel~ 4000 3 : Exper~ ECIS 8
4 5 R 256. F01,F02,F03 10,00~ 4000 1 : Exper~ ECIS 6
5 5 R 267. F04,F05,F06 10,00~ 4000 2 : Exper~ ECIS 6
6 5 R 265. F07,F08,F09 10,00~ 4000 3 : Exper~ ECIS 6
7 5 R 263. E01,E02,E03 15,00~ 4000 1 : Exper~ ECIS 5
8 5 R 280. E04,E05,E06 15,00~ 4000 2 : Exper~ ECIS 5
9 5 R 273. E07,E08,E09 15,00~ 4000 3 : Exper~ ECIS 5
10 5 R 272. D01,D02,D03 20,00~ 4000 1 : Exper~ ECIS 4
# i 926 more rows
# i 1 more variable: Excluded <chr>
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