Make a gp object

Usage

gp(rows = NULL, cols = NULL, data = NULL, wells = NULL, tidy = FALSE)

Arguments

rows: Numeric. The number of rows the plate should have.
cols: Numeric. The number of columns the plate should have.
data: An optional data.frame of well data the same dimensions as the plate to be described
wells: Numeric. The number of wells the plate has. If this is specified, rows and cols must be null - they are inferred from common form factors of plates.
tidy: Are the data supplied tidy?

Value

a gp object

Details

A gp object has the following components:

nrow/ncol: Number of plate rows/cols. This is static and will not be changed by adding layers.
well_data: Somewhat transient data used to define plotting coordinates for layers. See below for more information.
nrow_sec/ncols_sec: The number of rows/cols of the current section. When creating a plate, that number is the number of rows/cols of the plate (the plate is the section). Can take on a 'mar' suffix, which specifies the number including margins (if any)
nrow_sec_par/ncol_sec_par: The number of rows/cols of the parent section. When creating a plate, it has no parent, so defaults to being its own parent. Can take on a 'mar' suffix. See above.

well_data consists of many columns. The variable names can be broken down as follows:

row/col: row is always the y axis, col is always the x axis. By convention, plates start at 1, 1 in the top left corner.
sec: Short for 'section'. A section is a rectangular field of wells. sec alone refers to the number of the section itself. sec combined with row or col (eg row_sec) refers to the coordinates of a given well relative to it's section corners, with the top left corner of a given section always being (1, 1).
par: Short for 'parent'. These columns are all the data from the previous layer.
index: These specify (usually) multiwell strips only defined in one dimension. Together, index_row and index_col form checkerboard-like patterns, where each intersection is a section. This is a bit more complicated when wrap = TRUE, so the simile does not hold for all cases.

Examples


# If you specify wells, rows and columns are derived
# from a standard plate sizes:

gp(wells = 96)
#> 
#>                 12
#>    ________________________
#>   | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>   | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>   | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>   | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#> 8 | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>   | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>   | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>   | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#> 
#> 
#> Start corner: tl
#> Plate dimensions: 8 x 12

# As such, you cannot use the wells argument
# if you want to create more exotic plates:

try(gp(wells = 102))
#> Error in gp(wells = 102) : 
#>   wells is not of a known format (6, 12, 24, 48, 96, 384, 1536, or 3456)

# For that, you'll need to specify wells and cols:

gp(rows = 6, cols = 17)
#> 
#>                     17
#>    __________________________________
#>   | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>   | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>   | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#> 6 | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>   | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>   | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#> 
#> 
#> Start corner: tl
#> Plate dimensions: 6 x 17