label_plate_rowcol: Label a plate with sample and probe information

View source: R/plate_functions.R

label_plate_rowcolR Documentation

Label a plate with sample and probe information

Description

For more help, examples and explanations, see the plate setup vignette: vignette("platesetup_vignette", package = "tidyqpcr")

Usage

label_plate_rowcol(plate, rowkey = NULL, colkey = NULL, coercefactors = TRUE)

Arguments

plate

tibble (data frame) with variables well_row, well_col, well. This would usually be produced by create_blank_plate(). It is possible to include other information in additional variables.

rowkey

tibble (data frame) describing plate rows, with variables well_row and others.

colkey

tibble (data frame) describing plate columns, with variables well_col and others.

coercefactors

if TRUE, coerce well_row in rowkey and well_col in colkey to factors

Details

For worked examples of tidyqpcr analysis with 384-well plates, see: vignette("calibration_vignette", package = "tidyqpcr")

Value

tibble (data frame) with variables well_row, well_col, well, and others.

This tibble contains all combinations of well_row and well_col found in the input plate, and all information supplied in rowkey and colkey distributed across every well of the plate. Return plate is ordered by row well_row then column well_col.

Note this ordering may cause a problem if well_col is supplied as a character (1,10,11,...), instead of a factor or integer (1,2,3,...). For this reason, the function by default converts well_row in 'rowkey', and well_col in 'colkey', to factors, taking factor levels from 'plate', and messages the user.

If 'plate$well_col' or 'plate$well_row' are not factors and coercefactors = TRUE label_plate_rowcol will automatically convert them to factors, but will output a warning telling users this may lead to unexpected behaviour.

Other tidyqpcr functions require plate plans to contain variables sample_id, target_id, and prep_type, so 'label_plate_rowcol' will message if any of these are missing. This is a message, not an error, because these variables can be added by users later.

See Also

Other plate creation functions: create_blank_plate(), create_colkey_4diln_2ctrl_in_24(), create_colkey_6_in_24(), create_colkey_6diln_2ctrl_in_24(), create_rowkey_4_in_16(), create_rowkey_8_in_16_plain(), display_plate(), display_plate_qpcr(), display_plate_value(), make_row_names_echo1536(), make_row_names_lc1536()

Examples

label_plate_rowcol(plate = create_blank_plate()) # returns blank plate

# label blank 96-well plate with empty edge wells

label_plate_rowcol(plate = create_blank_plate(well_row = LETTERS[2:7], 
                                              well_col = 2:11))

# label 96-well plate with sample id in rows

label_plate_rowcol(plate = create_blank_plate(well_row = LETTERS[1:8],
                                              well_col = 1:12),
                   rowkey = tibble(well_row = LETTERS[1:8],
                                   sample_id = paste0("S_",1:8)))

# label fraction of 96-well plate with target id in columns

label_plate_rowcol(plate = create_blank_plate(well_row = LETTERS[1:8],
                                              well_col = 1:4),
                   colkey = tibble(well_col = 1:4,
                                   target_id = paste0("T_",1:4)))


ewallace/tidyqpcr documentation built on June 5, 2024, 10:04 a.m.