This is a function to easily input experimental design elements for later merging with read data
Usage
make_design(
nrows = NULL,
ncols = NULL,
block_row_names = NULL,
block_col_names = NULL,
block_name_header = "block_name",
output_format = "tidy",
wellnames_numeric = FALSE,
wellnames_sep = "",
wellnames_colname = "Well",
colnames_first = FALSE,
lookup_tbl_start = 1,
pattern_split = "",
...
)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
- block_name_header
The name of the field containing the
block_names- output_format
One of c("blocks", "blocks_pasted", "wide", "tidy") denoting the format of the resulting data.frame
For easy merging with tidymeasures, leave as default of 'tidy'.
For human-readability to confirm design is correct, choose 'blocks' or 'blocks_pasted'.
For writing to block-shaped file(s), choose 'blocks' or 'blocks_pasted'.
- wellnames_numeric
If
block_row_namesorblock_col_namesare not specified, then names will be generated automatically according towellnames_numeric.If
wellnames_numericis TRUE, rows and columns will be numbered with "R" and "C" prefixes, respectively.If
wellnames_numericis FALSE, rows will be lettered A through Z, while columns will be numbered- wellnames_sep
A string used when concatenating rownames and column names to create well names, when
output_format = "wide"oroutput_format = "tidy"- wellnames_colname
Header for newly-created column containing the well names, when
output_format = "tidy"- colnames_first
When wellnames are created for
output_format = "wide"oroutput_format = "tidy"by paste-ing the rownames and column names, should the column names come first.- 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, if they're not already a vector- ...
Each
...argument must be named, and 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 or vector denoting the pattern in which the values should be filled into the rows and columns specified.
If it's a string, will be split by
pattern_split. Pattern will be used as the indices of the values vector.0's refer to NA. The pattern will be recycled as necessary to fill all the wells of the rows and columns specified.
5. a logical for whether this pattern should be filled byrow
Value
Depends on output_format:
If output_format = "blocks", a list of data.frame's
where each data.frame is block-shaped containing the
information for a single design element
If output_format = "blocks_pasted", a single
data.frame containing the paste-ed information
for all design elements
If output_format = "wide", a wide-shaped data.frame
containing all the design elements
If output_format = "tidy", 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
make_design(nrows = 8, ncols = 12,
design_element_name = list(c("A", "B", "C"),
2:7,
2:11,
"112301",
TRUE))
#> Well design_element_name
#> 1 A1 <NA>
#> 2 A2 <NA>
#> 3 A3 <NA>
#> 4 A4 <NA>
#> 5 A5 <NA>
#> 6 A6 <NA>
#> 7 A7 <NA>
#> 8 A8 <NA>
#> 9 A9 <NA>
#> 10 A10 <NA>
#> 11 A11 <NA>
#> 12 A12 <NA>
#> 13 B1 <NA>
#> 14 B2 A
#> 15 B3 A
#> 16 B4 B
#> 17 B5 C
#> 18 B6 <NA>
#> 19 B7 A
#> 20 B8 A
#> 21 B9 A
#> 22 B10 B
#> 23 B11 C
#> 24 B12 <NA>
#> 25 C1 <NA>
#> 26 C2 <NA>
#> 27 C3 A
#> 28 C4 A
#> 29 C5 A
#> 30 C6 B
#> 31 C7 C
#> 32 C8 <NA>
#> 33 C9 A
#> 34 C10 A
#> 35 C11 A
#> 36 C12 <NA>
#> 37 D1 <NA>
#> 38 D2 B
#> 39 D3 C
#> 40 D4 <NA>
#> 41 D5 A
#> 42 D6 A
#> 43 D7 A
#> 44 D8 B
#> 45 D9 C
#> 46 D10 <NA>
#> 47 D11 A
#> 48 D12 <NA>
#> 49 E1 <NA>
#> 50 E2 A
#> 51 E3 A
#> 52 E4 B
#> 53 E5 C
#> 54 E6 <NA>
#> 55 E7 A
#> 56 E8 A
#> 57 E9 A
#> 58 E10 B
#> 59 E11 C
#> 60 E12 <NA>
#> 61 F1 <NA>
#> 62 F2 <NA>
#> 63 F3 A
#> 64 F4 A
#> 65 F5 A
#> 66 F6 B
#> 67 F7 C
#> 68 F8 <NA>
#> 69 F9 A
#> 70 F10 A
#> 71 F11 A
#> 72 F12 <NA>
#> 73 G1 <NA>
#> 74 G2 B
#> 75 G3 C
#> 76 G4 <NA>
#> 77 G5 A
#> 78 G6 A
#> 79 G7 A
#> 80 G8 B
#> 81 G9 C
#> 82 G10 <NA>
#> 83 G11 A
#> 84 G12 <NA>
#> 85 H1 <NA>
#> 86 H2 <NA>
#> 87 H3 <NA>
#> 88 H4 <NA>
#> 89 H5 <NA>
#> 90 H6 <NA>
#> 91 H7 <NA>
#> 92 H8 <NA>
#> 93 H9 <NA>
#> 94 H10 <NA>
#> 95 H11 <NA>
#> 96 H12 <NA>
## To be reminded what arguments are needed, use make_designpattern:
make_design(nrows = 8, ncols = 12,
design_element_name = make_designpattern(
values = c("A", "B", "C"),
rows = 2:7,
cols = 2:11,
pattern = "112301",
byrow = TRUE))
#> Well design_element_name
#> 1 A1 <NA>
#> 2 A2 <NA>
#> 3 A3 <NA>
#> 4 A4 <NA>
#> 5 A5 <NA>
#> 6 A6 <NA>
#> 7 A7 <NA>
#> 8 A8 <NA>
#> 9 A9 <NA>
#> 10 A10 <NA>
#> 11 A11 <NA>
#> 12 A12 <NA>
#> 13 B1 <NA>
#> 14 B2 A
#> 15 B3 A
#> 16 B4 B
#> 17 B5 C
#> 18 B6 <NA>
#> 19 B7 A
#> 20 B8 A
#> 21 B9 A
#> 22 B10 B
#> 23 B11 C
#> 24 B12 <NA>
#> 25 C1 <NA>
#> 26 C2 <NA>
#> 27 C3 A
#> 28 C4 A
#> 29 C5 A
#> 30 C6 B
#> 31 C7 C
#> 32 C8 <NA>
#> 33 C9 A
#> 34 C10 A
#> 35 C11 A
#> 36 C12 <NA>
#> 37 D1 <NA>
#> 38 D2 B
#> 39 D3 C
#> 40 D4 <NA>
#> 41 D5 A
#> 42 D6 A
#> 43 D7 A
#> 44 D8 B
#> 45 D9 C
#> 46 D10 <NA>
#> 47 D11 A
#> 48 D12 <NA>
#> 49 E1 <NA>
#> 50 E2 A
#> 51 E3 A
#> 52 E4 B
#> 53 E5 C
#> 54 E6 <NA>
#> 55 E7 A
#> 56 E8 A
#> 57 E9 A
#> 58 E10 B
#> 59 E11 C
#> 60 E12 <NA>
#> 61 F1 <NA>
#> 62 F2 <NA>
#> 63 F3 A
#> 64 F4 A
#> 65 F5 A
#> 66 F6 B
#> 67 F7 C
#> 68 F8 <NA>
#> 69 F9 A
#> 70 F10 A
#> 71 F11 A
#> 72 F12 <NA>
#> 73 G1 <NA>
#> 74 G2 B
#> 75 G3 C
#> 76 G4 <NA>
#> 77 G5 A
#> 78 G6 A
#> 79 G7 A
#> 80 G8 B
#> 81 G9 C
#> 82 G10 <NA>
#> 83 G11 A
#> 84 G12 <NA>
#> 85 H1 <NA>
#> 86 H2 <NA>
#> 87 H3 <NA>
#> 88 H4 <NA>
#> 89 H5 <NA>
#> 90 H6 <NA>
#> 91 H7 <NA>
#> 92 H8 <NA>
#> 93 H9 <NA>
#> 94 H10 <NA>
#> 95 H11 <NA>
#> 96 H12 <NA>