Description Usage Arguments Details Value Examples
A (square plate) layout assigning each cell (well) to a specific content with metadata to be taken from columns and/or rows parallel to the plate design.
1 2 3 4 5 6 7 8 9 10 11 | import_layout_from_excel(
file,
sheet = 1,
data_upper_left = "B3",
index_row = "2",
index_col = "A",
meta_row = c(concentration = "1"),
meta_col = character(),
plate_nrow = 16,
plate_ncol = 24
)
|
file |
A path or URL to an xlsx file or workbook. |
sheet |
The name or index of the sheet to read data from. |
data_upper_left |
A string specifying the top left corner (i.e. cell) in Excel coordinates of the plate. |
index_row |
A string specifying the row (in Excel coordinates) where the plate column index (e.g. running 1 through 24) is found. |
index_col |
A string specifying the column (in Excel coordinates) where the plate rows index (e.g. running A through P) is found. |
meta_row |
A named character vector to specify additional metadata to be assigned to each plate column. |
meta_col |
A named character vector to specify additional metadata to be assigned to each plate row. |
plate_nrow |
Number of rows to import starting from |
plate_ncol |
Number of columns to import starting from |
The content of each Excel cell of the plate is read as a string. Merged cells
are allowed and will be unmerged (see read.xlsx
).
When importing metadata, it is assumed that meta_row
and meta_col
run parallel to the plate. Offset is allowed. The category names of the metadata
must be specified explicitly during the setup; they are not imported.
In the example below, the first cell of the acutal plate is "B3". Three metadata columns are given: One in row "1" (here: Concentration), which is applied column-wise, and two parallel to the rows in column "Z" (here: Duplicate) and "AA" (here: Source). The name tags highlighted in yellow are not imported since they are not parallel to the actual plate rows. So is the text "xyz" shown in red.
A tibble
in long form with the columns well
,
well_let
(letters, row index of the plate), well_num
(integers
as strings, column index of the plate), content
and a column for each
metadata specified.
#'
1 2 3 4 5 6 7 8 | layout_file <- system.file("extdata", "platelayout_maldi.xlsx", package = "summerrmass")
import_layout_from_excel(layout_file,
# metadata stored in row number "1" (Excel coordinates) contains concentration
meta_row = c(Concentration = 1),
# metadata stored in column "Z" (Excel coordinates) contains rowwise metadata;
# missing values are "NA", the order in meta_col determines the column arrangement
meta_col = c(Source = "AA", Duplicates = "Z"))
|
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