Plate formatting functions • fpcountr

Functions like find_wells_in_row(), find_wells_in_column(), and find_wells_in_rowcolumn() are helper functions that can be useful for avoiding manually writing out lists of wells when processing experimental data.

library(fpcountr)

find_wells_in_row(rows = c("A", "D"), plate_type = 96)

##  [1] "A1"  "A2"  "A3"  "A4"  "A5"  "A6"  "A7"  "A8"  "A9"  "A10" "A11" "A12"
## [13] "D1"  "D2"  "D3"  "D4"  "D5"  "D6"  "D7"  "D8"  "D9"  "D10" "D11" "D12"

find_wells_in_column(columns = c(1,2), plate_type = 24)

## [1] "A1" "A2" "B1" "B2" "C1" "C2" "D1" "D2"

find_wells_in_rowcolumn(rows = c("A", "B"), columns = c(1, 11,12), plate_type = 96)

## [1] "A1"  "A11" "A12" "B1"  "B11" "B12"

There is also find_wells() which lets you print all of the wells in a given plate type.

find_wells(plate_type = 96)

##  [1] "A1"  "A2"  "A3"  "A4"  "A5"  "A6"  "A7"  "A8"  "A9"  "A10" "A11" "A12"
## [13] "B1"  "B2"  "B3"  "B4"  "B5"  "B6"  "B7"  "B8"  "B9"  "B10" "B11" "B12"
## [25] "C1"  "C2"  "C3"  "C4"  "C5"  "C6"  "C7"  "C8"  "C9"  "C10" "C11" "C12"
## [37] "D1"  "D2"  "D3"  "D4"  "D5"  "D6"  "D7"  "D8"  "D9"  "D10" "D11" "D12"
## [49] "E1"  "E2"  "E3"  "E4"  "E5"  "E6"  "E7"  "E8"  "E9"  "E10" "E11" "E12"
## [61] "F1"  "F2"  "F3"  "F4"  "F5"  "F6"  "F7"  "F8"  "F9"  "F10" "F11" "F12"
## [73] "G1"  "G2"  "G3"  "G4"  "G5"  "G6"  "G7"  "G8"  "G9"  "G10" "G11" "G12"
## [85] "H1"  "H2"  "H3"  "H4"  "H5"  "H6"  "H7"  "H8"  "H9"  "H10" "H11" "H12"

find_wells(plate_type = 24)

##  [1] "A1" "A2" "A3" "A4" "A5" "A6" "B1" "B2" "B3" "B4" "B5" "B6" "C1" "C2" "C3"
## [16] "C4" "C5" "C6" "D1" "D2" "D3" "D4" "D5" "D6"

The most common use case for these functions is when you use process_plate() to process data from a plate experiment. Say you have your blank wells in column 11, and your negative wells in rows G-H, columns 1-4:

processed_data <- process_plate(
  data_csv = "data/example_experiment_parsed.csv",
  blank_well = find_wells_in_column(11),
  od_name = "OD700",
  flu_channels = c("blue"),
  af_model = "spline",
  neg_well = find_wells_in_rowcolumn(rows = c("G", "H"), columns = c(1,2,3,4)),
  outfolder = "experiment_analysis"
)

Similarly, in calc_fppercell() when you are given the option to remove wells unneeded in the analysis, such as those that contain media or that were empty, you can use these functions to save a lot of typing.

pc_data_mTagBFP2 <- calc_fppercell(
  data_csv = "experiment_analysis/example_experiment_parsed_processed.csv",
  flu_channels = c("blue"),
  flu_labels = c("mTagBFP2"),
  remove_wells = c(find_wells_in_column(11), # media
                   find_wells_in_column(c(1,12)) # empty wells
  ),
  outfolder = "experiment_analysis"
)