vascr: Process Biological Impedance Sensing Data

Find varous things

Code
  vascr_find_normalised(standard)
Output
  [1] FALSE

Code
  vascr_find_normalised(normal)
Output
  [1] 100

Force median

Code
  vascr:::vascr_force_median(c(1, 3, 5, 6), "up")
Output
  [1] 5

Code
  vascr:::vascr_force_median(c(1, 3, 5, 6), "down")
Output
  [1] 3

Vascr match

Code
  vascr_match("Re", vector)
Message
  ! [Re] corrected to [Rb]. Please check the argeuments for your functions are correctly typed.
Output
  [1] "Rb"

Code
  vascr_match("Rb", vector)
Output
  [1] "Rb"

Code
  vascr_match(c("Rb", "Cm"), vector)
Output
  [1] "Rb" "Cm"

vascr_find_single_time

Code
  vascr_find_single_time(growth.df, NULL)
Output
   [1]   0   5  10  15  20  25  30  35  40  45  50  55  60  65  70  75  80  85  90
  [20]  95 100 105 110 115 120 125 130 135 140 145 150 155 160 165 170 175 180 185
  [39] 190 195 200

Code
  vascr_find_single_time(growth.df, c(1, 3))
Message
  ! Vascr_find_single_time deals with only one time in one call. Use find times if more parsing is needed.
Output
  [1] "NA"

Code
  vascr_find_single_time(c(1, 2, 3), c(1, 3))
Message
  ! Vascr_find_single_time deals with only one time in one call. Use find times if more parsing is needed.
Output
  [1] "NA"

Code
  vascr_find_single_time(growth.df, c(4.876))
Message
  ! [ 4.876 ]  corrected to  [ 5 ]. Please check the variables used.
Output
  [1] 5

vascr_find_well

Code
  vascr_find_well(growth.df, NULL)
Output
   [1] "A01" "A02" "A03" "B01" "B02" "B03" "C01" "C02" "C03" "D01" "D02" "D03"
  [13] "E01" "E02" "E03" "F01" "F02" "F03" "G01" "G02" "G03" "H01" "H02" "H03"
  [25] "A04" "A05" "A06" "B04" "B05" "B06" "C04" "C05" "C06" "D04" "D05" "D06"
  [37] "E04" "E05" "E06" "F04" "F05" "F06" "G04" "G05" "G06" "H04" "H05" "H06"
  [49] "A07" "A08" "A09" "B07" "B08" "B09" "C07" "C08" "C09" "D07" "D08" "D09"
  [61] "E07" "E08" "E09" "F07" "F08" "F09" "G07" "G08" "G09" "H07" "H08" "H09"

Code
  vascr_find_well(growth.df, "A01")
Output
  [1] "A01"

Code
  vascr_find_well(growth.df, "A1")
Output
  [1] "A01"

Code
  vascr_find_well(growth.df, "W39")
Message
  ! Well NA is not a valid well name, please check your input data
  ! [NA] corrected to [A01]. Please check the argeuments for your functions are correctly typed.
Output
  [1] "A01"

vascr_find_time

Code
  vascr_find_time(growth.df, NULL)
Output
   [1]   0   5  10  15  20  25  30  35  40  45  50  55  60  65  70  75  80  85  90
  [20]  95 100 105 110 115 120 125 130 135 140 145 150 155 160 165 170 175 180 185
  [39] 190 195 200

Code
  vascr_find_time(growth.df, list(1, 3, 5))
Message
  ! [ 1 ]  corrected to  [ 0 ]. Please check the variables used.
  ! [ 3 ]  corrected to  [ 5 ]. Please check the variables used.
Output
  [1] 0 5 5

Code
  vascr_find_time(growth.df, Inf)
Output
   [1]   0   5  10  15  20  25  30  35  40  45  50  55  60  65  70  75  80  85  90
  [20]  95 100 105 110 115 120 125 130 135 140 145 150 155 160 165 170 175 180 185
  [39] 190 195 200

Code
  vascr_find_time(growth.df, c(10, 20))
Output
  [1] 10 15 20

Code
  vascr_find_time(growth.df, 5)
Output
  [1] 5

Code
  vascr_find_time(growth.df, NA)
Output
  [1] 100

vascr_find_frequency

Code
  vascr_find_frequency(growth.df, 4382)
Message
  ! Frequency corrected from 4382 to 4000
Output
  [1] 4000

Code
  vascr_find_frequency(growth.df, 4000)
Output
  [1] 4000

Code
  vascr_find_frequency(growth.df, NULL)
Output
   [1]     0  1000 16000  2000   250 32000  4000   500 64000  8000

Code
  vascr_find_frequency(growth.df, NA)
Output
  [1] 4000

Code
  vascr_find_frequency(growth.df, Inf)
Output
  [1] Inf

Code
  vascr_find_frequency(growth.df, "raw")
Output
  [1]  1000 16000  2000   250 32000  4000   500 64000  8000

Code
  vascr_find_frequency(growth.df, "model")
Output
  [1] 0

vascr_instrument_list

Code
  vascr_instrument_list()
Output
  [1] "ECIS"        "xCELLigence" "cellZscope"

vascr_units_table

Code
  vascr_units_table()
Output
      Unit                          Content Modeled  Instrument
  1  Alpha           Alpha (ohm cm squared)    TRUE        ECIS
  2     Cm     Cm (microfarad / cm squared)    TRUE        ECIS
  3  Drift                        Drift (%)    TRUE        ECIS
  4     Rb              Rb (chm cm squared)    TRUE        ECIS
  5   RMSE                   Model Fit RMSE    TRUE        ECIS
  6      C         Capacatance (microfarad)   FALSE        ECIS
  7      C         Capacatance (microfarad)   FALSE  cellZscope
  8      P            Phase (radians, 0 Hz)   FALSE        ECIS
  9      P            Phase (radians, 0 Hz)   FALSE  cellZscope
  10     R           Resistance (ohm, 0 Hz)   FALSE        ECIS
  11     R           Resistance (ohm, 0 Hz)   FALSE  cellZscope
  12     X Capacative Reactance (ohm, 0 Hz)   FALSE        ECIS
  13     X Capacative Reactance (ohm, 0 Hz)   FALSE  cellZscope
  14     Z            Impedance (ohm, 0 Hz)   FALSE        ECIS
  15     Z            Impedance (ohm, 0 Hz)   FALSE xCELLigence
  16     Z            Impedance (ohm, 0 Hz)   FALSE  cellZscope
  17    CI                       Cell Index   FALSE xCELLigence
  18 CPE_A         Capacatance (microfarad)    TRUE  cellZscope
  19 CPE_n                            CPE_n    TRUE  cellZscope
  20   TER             TER (ohm cm squared)    TRUE  cellZscope
  21   Ccl    Ccl (microFarad / cm squared)    TRUE  cellZscope
  22  Rmed                       Rmed (ohm)    TRUE  cellZscope

vascr_find_instrument

Code
  vascr_find_instrument(growth.df, "Rb")
Message
  ! [Rb] corrected to [ECIS]. Please check the argeuments for your functions are correctly typed.
Output
  [1] "ECIS"

Code
  vascr_find_instrument(growth.df, NULL)
Output
  [1] "ECIS"

Code
  vascr_find_instrument(growth.df, "cellZscope")
Message
  ! cellZscope data is not present in the dataset. Use with care
  ! No selected instruments present in dataset. Use with care.
Output
  NULL

Code
  vascr_find_instrument(growth.df, c("cellZscope", "ECIS"))
Message
  ! cellZscope data is not present in the dataset. Use with care
Output
  [1] "ECIS"

Code
  vascr_find_instrument(growth.df, c("cellZscope", "xCELLigence"))
Message
  ! cellZscope data is not present in the dataset. Use with care
  ! xCELLigence data is not present in the dataset. Use with care
  ! No selected instruments present in dataset. Use with care.
Output
  NULL

vascr_find_unit

Code
  vascr_find_unit(growth.df, "raw")
Output
  [1] "C" "P" "R" "X" "Z"

Code
  vascr_find_unit(growth.df, "modeled")
Output
  [1] "Alpha" "Cm"    "Drift" "Rb"    "RMSE"

Code
  vascr_find_unit(growth.df, "all")
Output
   [1] "Alpha" "Cm"    "Drift" "Rb"    "RMSE"  "C"     "P"     "R"     "X"    
  [10] "Z"

Code
  vascr_find_unit(growth.df, "Cm")
Output
  [1] "Cm"

Code
  vascr_find_unit(growth.df, NULL)
Output
   [1] "Alpha" "Cm"    "Drift" "Rb"    "RMSE"  "C"     "P"     "R"     "X"    
  [10] "Z"

Code
  vascr_find_unit(growth.df, unit = c("Ci", "Rb"))
Message
  ! [Ci] corrected to [Cm]. Please check the argeuments for your functions are correctly typed.
Output
  [1] "Cm" "Rb"

Code
  vascr_find_unit(growth.df, NA)
Output
  [1] "R"

Code
  vascr_find_unit(growth.df %>% mutate(Instrument = "cellZscope"), NA)
Output
  [1] "TER"

Code
  vascr_find_unit(growth.df %>% mutate(Instrument = "xCELLigence"), NA)
Output
  [1] "CI"

vascr_find_experiment

Code
  vascr_find_experiment(growth.df, 1)
Output
  [1] "1 : Experiment 1"

Code
  vascr_find_experiment(growth.df, "1 : Experiment 1")
Output
  [1] "1 : Experiment 1"

Code
  vascr_find_experiment(growth.df, NULL)
Output
  [1] 1 : Experiment 1 2 : Experiment2  3 : Experiment3 
  Levels: 1 : Experiment 1 2 : Experiment2 3 : Experiment3

vascr_titles render

Code
  vascr_titles(unit, frequency)
Output
  Capacitance (nF, 1000 Hz)

Code
  vascr_titles(unit, frequency)
Output
  Resistance (ohm, 1000 Hz)

Code
  vascr_titles(unit, frequency)
Output
  Phase (radians, 1000 Hz)

Code
  vascr_titles(unit, frequency)
Output
  Capacative Reactance (ohm, 1000 Hz)

Code
  vascr_titles(unit, frequency)
Output
  Impedance (ohm, 1000 Hz)

Code
  vascr_titles(unit, frequency)
Output
  Rb (ohm cm<sup>2</sup>)

Code
  vascr_titles(unit, frequency)
Output
  Cm (&#956;F/cm<sup>2</sup>)

Code
  vascr_titles(unit, frequency)
Output
  ohm<sup>1/2</sup> cm

Code
  vascr_titles(unit, frequency)
Output
  Model Fit RMSE

Code
  vascr_titles(unit, frequency)
Output
  Drift (%)

Code
  vascr_titles(unit, frequency)
Output
  Cell Index

Code
  vascr_titles(unit, frequency)
Output
  CPE_A (s<sup>n-1</sup>&#956;F/cm<sup>2</sup>)

Code
  vascr_titles(unit, frequency)
Output
  CPE_n

Code
  vascr_titles(unit, frequency)
Output
  TER (&#937; cm<sup>2</sup>)

Code
  vascr_titles(unit, frequency)
Output
  Ccl (&#956;F/cm<sup>2</sup>)

Code
  vascr_titles(unit, frequency)
Output
  Rmed (ohm)

vascr_titles

Code
  vascr_titles("random text, not changed")
Output
  [1] "random text, not changed"

Code
  vascr_titles_vector(c("Rb", "R", "Cm"))
Output
  [1] "Rb (chm cm squared)"          "Resistance (ohm, 0 Hz)"      
  [3] "Cm (microfarad / cm squared)"

Code
  vascr_instrument_units("ECIS")
Output
   [1] "Alpha" "Cm"    "Drift" "Rb"    "RMSE"  "C"     "P"     "R"     "X"    
  [10] "Z"

Code
  vascr_instrument_units("xCELLigence")
Output
  [1] "Z"  "CI"

Code
  vascr_instrument_units("cellZscope")
Output
   [1] "CPE_A" "CPE_n" "TER"   "Ccl"   "Rmed"  "C"     "P"     "R"     "X"    
  [10] "Z"

Code
  vascr_instrument_from_unit("Rb")
Output
  [1] "ECIS"

Code
  vascr_instrument_from_unit("CI")
Output
  [1] "xCELLigence"

Code
  vascr_instrument_from_unit("TER")
Output
  [1] "cellZscope"

test if data is summarised

Code
  vascr_find_level(growth.df)
Output
  [1] "wells"

Code
  vascr_find_level(vascr_summarise(growth.df, level = "experiments"))
Output
  [1] "experiments"

Code
  vascr_find_level(vascr_summarise(growth.df, level = "summary"))
Output
  [1] "summary"

test vascr file validation

Code
  vascr_validate_file(test_file_path, "abp")
Output
  [1] TRUE

Code
  vascr_validate_file(test_file_path, extension = c("abp", "r"))
Output
  [1] TRUE

test well standardisation

Code
  vascr_standardise_wells("A01")
Output
  [1] "A01"

Code
  vascr_standardise_wells("A 1")
Output
  [1] "A01"

Code
  vascr_standardise_wells("tortoise")
Message
  ! Well NA is not a valid well name, please check your input data
Output
  [1] "NA"

Code
  vascr_standardise_wells(growth.df$Well) %>% head()
Output
  [1] "A01" "A02" "A03" "B01" "B02" "B03"

96 well names are correct

Code
  vascr_96_well_names()
Output
   [1] "A01" "B01" "C01" "D01" "E01" "F01" "G01" "H01" "A02" "B02" "C02" "D02"
  [13] "E02" "F02" "G02" "H02" "A03" "B03" "C03" "D03" "E03" "F03" "G03" "H03"
  [25] "A04" "B04" "C04" "D04" "E04" "F04" "G04" "H04" "A05" "B05" "C05" "D05"
  [37] "E05" "F05" "G05" "H05" "A06" "B06" "C06" "D06" "E06" "F06" "G06" "H06"
  [49] "A07" "B07" "C07" "D07" "E07" "F07" "G07" "H07" "A08" "B08" "C08" "D08"
  [61] "E08" "F08" "G08" "H08" "A09" "B09" "C09" "D09" "E09" "F09" "G09" "H09"
  [73] "A10" "B10" "C10" "D10" "E10" "F10" "G10" "H10" "A11" "B11" "C11" "D11"
  [85] "E11" "F11" "G11" "H11" "A12" "B12" "C12" "D12" "E12" "F12" "G12" "H12"

vascr_gg_hue

Code
  vascr_gg_color_hue(5)
Output
  [1] "#F8766D" "#9BA800" "#00C08F" "#00A7FF" "#F862DE"

vascr_colnames_works

Code
  vascr_cols()
Output
   [1] "Time"       "Unit"       "Value"      "Well"       "Sample"    
   [6] "Frequency"  "Experiment" "Instrument" "SampleID"   "Excluded"

Code
  vascr_cols(growth.df, set = "exploded")
Output
  [1] "cells" "line"

Code
  vascr_cols(growth.df, set = "core")
Output
   [1] "Time"       "Unit"       "Value"      "Well"       "Sample"    
   [6] "Frequency"  "Experiment" "Instrument" "SampleID"   "Excluded"

Code
  vascr_cols(growth.df, set = "not_a_set")
Message
  ! Inappropriate set selected, please use another
Output
  NULL

Find metadata works

Code
  vascr_find_metadata(growth.df)
Message

  Timepoints

JamesHucklesby/vascr documentation built on July 16, 2025, 8:16 p.m.

rdrr.io home R language documentation Run R code online

CRAN packages Bioconductor packages R-Forge packages GitHub packages

Note that we can't provide technical support on individual packages. You should contact the package authors for that.

JamesHucklesby/vascr
Process Biological Impedance Sensing Data

tests/testthat/_snaps/vascr_find.md
In JamesHucklesby/vascr: Process Biological Impedance Sensing Data

Find varous things

Force median

Vascr match

vascr_find_single_time

vascr_find_well

vascr_find_time

vascr_find_frequency

vascr_instrument_list

vascr_units_table

vascr_find_instrument

vascr_find_unit

vascr_find_experiment

vascr_titles render

vascr_titles

test if data is summarised

test vascr file validation

test well standardisation

96 well names are correct

vascr_gg_hue

vascr_colnames_works

Find metadata works

R Package Documentation

Browse R Packages

We want your feedback!

JamesHucklesby/vascr Process Biological Impedance Sensing Data

tests/testthat/_snaps/vascr_find.md In JamesHucklesby/vascr: Process Biological Impedance Sensing Data

Find varous things

Force median

Vascr match

vascr_find_single_time

vascr_find_well

vascr_find_time

vascr_find_frequency

vascr_instrument_list

vascr_units_table

vascr_find_instrument

vascr_find_unit

vascr_find_experiment

vascr_titles render

vascr_titles

test if data is summarised

test vascr file validation

test well standardisation

96 well names are correct

vascr_gg_hue

vascr_colnames_works

Find metadata works

R Package Documentation

Browse R Packages

We want your feedback!

JamesHucklesby/vascr
Process Biological Impedance Sensing Data

tests/testthat/_snaps/vascr_find.md
In JamesHucklesby/vascr: Process Biological Impedance Sensing Data