Package 'gplate'

Arrange gp well data relative to user supplied start_corner

Description

Arrange gp well data relative to user supplied start_corner

Usage

arrange_by_dim(gp, dim)

Arguments

gp	A gp object
dim	Character. Either "row" or "col"

Value

A gp with gp$well_data arranged by dim and the non-dim (ie if dim = "row", the 'non-dim' is "col") relative to the start corner (start corner is at the top, farther from start corner is at bottom)

---

Coerce object to gp

Description

Coerce object to gp

Usage

as_gp(x, ...)

## Default S3 method:
as_gp(x, ...)

## S3 method for class 'list'
as_gp(x, ...)

Arguments

x	Object to coerce
...	Unused

---

Create a dimension pattern 'unit' of a section

Description

Create a dimension pattern 'unit' of a section

Usage

coordinate(gp, type = c("row", "col"), margin)

Arguments

gp	a gp
type	Character. Either 'row' or 'col'.
margin	Named list of integers defining the size of margins at each edge.

Value

a tibble

---

A 8x12 matrix of random integers 1-10

Description

A 8x12 matrix of random integers 1-10

Usage

example_plate

Format

An object of class matrix (inherits from array) with 8 rows and 12 columns.

---

Take a set of numbers and flip them around on a number line

Description

Take a set of numbers and flip them around on a number line

Usage

flip_dim(gp, dim)

Arguments

gp	A gp
dim	Symbol. Column to flip. Should be the name of a column that exists in gp$well_data

Details

This assumes the beginning is 1 and the end is maximum length of the dimension. Note that this does NOT simply check the maximum value of the supplied vector, but searches the supplied gp for a matching ndim column that definitively tells how long the given dimension is supposed to be. This is important, as sometimes a dimension is given that is longer than its parent dimension, so the maximum numbers would not show in the vector.

Value

A vector.

---

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)

---

Slice out a smaller gp from a gp via coordinates

Description

Slice out a smaller gp from a gp via coordinates

Usage

gp_excise(gp, top, left, bottom, right)

Arguments

gp	A gp
top, left, bottom, right	Integer. The coordinates of the corners. Remember that TOP left is (1, 1)

Value

A gp with top left coords = (1, 1)

Examples

gplate::example_plate |> as_gp() |> gp_excise(2, 2, 4, 4)

---

A theme for making little in-line plots

Description

A theme for making little in-line plots

Usage

gp_mini_theme()

Value

A ggplot2 theme

---

Plot a gp object

Description

Plot a gp object

Usage

gp_plot(x, name = .sec, ...)

## S3 method for class 'gp'
gp_plot(x, name = .sec, ...)

## S3 method for class 'data.frame'
gp_plot(x, name = .sec, ...)

Arguments

x	A gp object or data.frame
name	Symbol. Name of a column in gp$well_data (or a column in the data.frame if data.frame was supplied) to use as a color.
...	Additional arguments to be passed to ggplot2::geom_point()

Value

a ggplot

Examples

gp(16, 24) |> gp_plot(.row)

---

Add a section to a gp object.

Description

Add a section to a gp object.

Usage

gp_sec(gp, ...)

## S3 method for class 'gp'
gp_sec(
  gp,
  name,
  nrow = NULL,
  ncol = NULL,
  labels = NULL,
  start_corner = c("tl", "tr", "bl", "br"),
  flow = c("row", "col"),
  margin = 0,
  wrap = FALSE,
  break_sections = TRUE,
  advance = TRUE
)

Arguments

gp	A gp object
name	Character. Name of the section.
nrow	Numeric. Section height. If NULL, will fill width of parent section.
ncol	Numeric. Section width. If NULL, will fill width of parent section.
labels	Optional. What should the labels of each section be?
start_corner	Corner of section to place first item.
flow	Direction that subsequent items should be placed relative to first corner.
margin	Border width outside the section that will be unfilled. Can take an argument of one (same border all around), two (top/bottom, left/right), three (top, left/right, bottom), or four (top, right, bottom, left).
wrap	Should the sections that go off the edge continue on the next row/column?
break_sections	Should partial sections be allowed?
advance	Should this section be a child or sibling of the one before it? If TRUE (default), it will be a child.

Value

a gp

Examples

gp(16, 24) |> gp_sec("section 1", ncol = 3)

pq <- gp(8, 12, protein_quant) |> gp_sec("has_sample", 3, 19, wrap = TRUE, labels = "sample")

# Sections can be used to label things for tidying
pq |> gp_serve()

# They can also be used for plotting:
pq |> gp_plot(has_sample)

---

Extract useful, tidy data from a gp object

Description

Extract useful, tidy data from a gp object

Usage

gp_serve(gp)

Arguments

gp

a gp

Value

a tibble, with .row and .col, as well as any created section names and data values.

Examples

gp(16, 24) |>
  gp_sec("my_sec", nrow = 9, ncol = 7, labels = c("sample_1", "sample_2", "sample_3")) |>
  gp_serve()

---

Turn data from 'plate form' to 'tidy form' and back

Description

Turn data from 'plate form' to 'tidy form' and back

Usage

gp_unravel(df, rownames = NULL)

gp_reravel(df, row_name = ".row", col_name = ".col", values = "value")

Arguments

df	The data.frame in plate-form to be tidied
rownames	Optional character. If there is a colname that specifies the row index, it will be arranged by this column, then dropped.

Value

a tibble

Examples

test_plate <- matrix(sample(1:10, 96, replace = TRUE), nrow = 8, ncol = 12)

gp_unravel(test_plate)

---

Turn a tidy data.frame into a gp

Description

An opposite to serve()

Usage

gp_unserve(x, row = ".row", col = ".col", nrow = NULL, ncol = NULL)

Arguments

x	A tidy data.frame representation of plate data
row	Character. The column that represents the rows. Should be numeric, with the lowest number representing the topmost row.
col	Character. The name of the column that represents columns. Should be numeric, with the lowest number representing the leftmost column.
nrow	Optional numeric, denoting the number of rows in the plate. If not supplied, will be imputed from the largest number in the 'row' column
ncol	Optional numeric, denoting the number of columns in the plate. If not supplied, will be imputed from the largest number in the 'col' column

Value

a gp

---

Check if axis moves in the canonical direction

Description

'Forwards' is thought of 'left to right' when thinking about moving across columns and 'top to bottom' when moving across rows

Usage

is_fwd(gp, dim)

Arguments

gp	A gp
dim	Character. A dimension, either "row" or "col".

Value

logical.

---

A constructor for a gp object

Description

A constructor for a gp object

Usage

new_gp(nrow = 1L, ncol = 1L, data = data.frame(), tidy = FALSE)

Arguments

nrow	Integer. Number of rows of the plate.
ncol	Integer. Number of columns of the plate.
data	An optional dataframe including plate data
tidy	Is the supplied data already tidy, or should it be tidied?

Value

a gp object

Examples

new_gp(nrow = 8L, ncol = 16L)

---

Recycle a df a non-integer number of times

Description

Recycle a df a non-integer number of times

Usage

non_int_replicate(df, measure)

Arguments

df	data.frame to be replicated
measure	Length-out of replication (not number of times). Can be a numeric, a vector, or a df. If a df, will use number of rows. If a vector, will use length.

Value

a data.frame with nrow measure

---

Data from a PCR experiment on a 384-well plate

Description

Data from a PCR experiment on a 384-well plate

Usage

pcr_plate

Format

An object of class matrix (inherits from array) with 16 rows and 24 columns.

---

Standard plate formats for microwell plates

Description

Standard plate formats for microwell plates

Usage

plate_formats

Format

An object of class data.frame with 9 rows and 3 columns.

---

Data from a protein quantification assay in a 96-well plate. See the "Using gp to wrangle plate data" vignette for more details

Description

Data from a protein quantification assay in a 96-well plate. See the "Using gp to wrangle plate data" vignette for more details

Usage

protein_quant

Format

An object of class matrix (inherits from array) with 8 rows and 12 columns.

---

Performs flip_dim if necessary

Description

Performs flip_dim if necessary

Usage

rel_dim(gp, dim, rel)

Arguments

gp	A gp
dim	Symbol. Column to conditionally flip. Should be the name of a column that exists in gp$well_data
rel	Character. Column to check if_fwd on. If TRUE, return dim as is. If FALSE (rel is backwards), flip the column.

Value

A vector that is flipped (see flip_dim) if rel is backwards (see is_fwd)

---

Repeat one dimension of a child section across a dimension of a parent section

Description

Repeat one dimension of a child section across a dimension of a parent section

Usage

unroll_sec_dim_along_parent(gp, dim, wrap)

Arguments

gp	A gp
dim	Either "row" or "col"
wrap	Logical. Should this dimension wrap around when it hits a section boundary?

Value

A gp

---

Extract well data from an object

Description

Extract well data from an object

Usage

well_data(x, ...)

## S3 method for class 'gp'
well_data(x, ...)

Arguments

x	An object to be passed to its respective method
...	Additional arguments (unused)

Value

A tibble containing the well data of the object

---

Calculate wells of gp object

Description

Calculate wells of gp object

Usage

wells(x, ...)

## S3 method for class 'gp'
wells(x, ...)

Arguments

x	a gp
...	Unused

---