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Make tidy design data.frame's

Source: R/functions.R
make_tidydesign.Rd

This is a function to easily input experimental design elements for later merging with read data

Usage

make_tidydesign(
  nrows = NULL,
  ncols = NULL,
  block_row_names = NULL,
  block_col_names = NULL,
  wellnames_sep = "",
  wellnames_colname = "Well",
  wellnames_Excel = TRUE,
  lookup_tbl_start = 1,
  pattern_split = "",
  colnames_first = FALSE,
  ...
)

Arguments

nrows, ncols

Number of rows and columns in the plate data

block_row_names, block_col_names

Names of the rows, columns of the plate blockmeasures data

wellnames_sep

A string used when concatenating rownames and column names to create well names

wellnames_colname

Header for newly-created column containing the well names

wellnames_Excel

If block_row_names or block_col_names are not specified, should rows and columns be named using Excel-style base-26 lettering for rows and numbering for columns? If FALSE, rows and columns will be numbered with "R" and "C" prefix.

lookup_tbl_start

Value in the lookup table for the split pattern values that corresponds to the first value in the vector.

Lookup table by default is c(1,2,...,8,9,A,B,...Y,Z,a,b,...,y,z). If, for example, lookup_tbl_start = "A", then the lookup table will now be c(A,B,...Y,Z,a,b,...,y,z)

pattern_split

character to split pattern elements provided in ... by

colnames_first

In the wellnames created by paste-ing the rownames and column names, should the column names come first

...

Each ... argument must be a list with five elements:

  1. a vector of the values

  2. a vector of the rows the pattern should be applied to

  3. a vector of the columns the pattern should be applied to

  4. a string of the pattern itself, where numbers refer to the indices in the values vector

    0's refer to NA

    This pattern will be split using pattern_split, which defaults to every character

  5. a logical for whether this pattern should be filled byrow

Value

a tidy-shaped data.frame containing all the design elements

Details

Note that either nrows or block_row_names must be provided and that either ncols or block_col_names must be provided

Examples:

my_example <- make_tidydesign(nrows = 8, ncols = 12,
    design_element_name = list(c("Value1", "Value2", "Value3"),
                      rowstart:rowend, colstart:colend,
                      "111222333000", TRUE)

To make it easier to pass arguments, use make_designpattern:

my_example <- make_tidydesign(nrows = 8, ncols = 12,
  design_element_name = make_designpattern(values = c("L", "G", "C"),
                                            rows = 2:7, cols = 2:11,
                                            pattern = "11223300",
                                            byrow = TRUE))