gp: Make a gp object

In KaiAragaki/Plate: A Grammar of Plates

Make a gp object

Description

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?

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.

Value

a gp object

Examples

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

gp(wells = 96)

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

try(gp(wells = 102))

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

gp(rows = 6, cols = 17)

KaiAragaki/Plate documentation built on Sept. 2, 2024, 3:39 a.m.