plateMap: Generate a set of plate maps for genotyping
In smgogarten/PlateMap: Create genotyping plate maps

Description Usage Arguments Details Value Author(s) Examples

Assigns samples to plates for genotyping, balancing important variables across plates.

plateMap(sample.data, plate.data, duplicates=NULL,
         empty.wells.at.end=TRUE,
         families.at.random=TRUE,
         debug=FALSE)

`sample.data`	A data.frame with sample data, including "SampleID," and as many other columns as there are categories on which to stratify the plate maps. If there are no other columns, the plate map will be completly random. An optional column called "Reserve" is a logical variable for samples that should be distributed evenly across plates outside of stratification (such as cross-study duplicates or WGA samples). If families should be plated together, give family ID in column "Family."
`plate.data`	A data frame with columns "Plate," "Well," and "SampleID." If any wells are to be reserved for controls, they should have a non-empty value in the "SampleID" column. Available wells should have an empty string ("") in the "SampleID" column.
`duplicates`	A data.frame with two columns, where the SampleID in column two is the duplicate of the SampleID in column one. If this argument is provided, duplicates will not be placed on the same plate and the ids from column two will be evenly balanced across plates. SampleIDs in both columns should be present in `sample.data`.
`empty.wells.at.end`	A logical. If `TRUE`, all empty wells will be adjacent on the last plate. If `FALSE`, empty wells will be randomly distributed across plates.
`families.at.random`	A logical. If `TRUE`, families will be plated at random, with the constraint that all members of the family will fit on the plate. If `FALSE`, plates for families will be selected in order of the number of empty wells, such that all plates will have at least one family before any plate has more than one family.
`debug`	A logical. If `TRUE`, the the "random" sampling of sample ids & well positions will be taken from a previously set seed, so repeated runs of the function will generate the same results.

The plates will be balanced so that the fraction of samples in each category given in sample.data on each plate mirrors the total fraction in the sample set as closely as possible.

The data.frame in plate.data, with the "SampleID" column filled in with values from sample.data.

Stephanie M. Gogarten, Caitlin McHugh, David Levine

head(plate.data)
head(sample.data)
head(duplicate.data)
sample.group <- sample.data[,c("SampleID", "Group", "Sex")]
map <- plateMap(sample.group, plate.data, duplicate.data, debug=TRUE)
tmp <- merge(map, sample.group)
table(tmp$Plate, paste(tmp$Sex, tmp$Group, sep="."))

sample.family <- sample.data[,c("SampleID", "Family", "Group")]
map <- plateMap(sample.family, plate.data, duplicate.data, debug=TRUE)
tmp <- merge(map, sample.family)
head(tmp[order(tmp$Family),])
table(tmp$Plate, tmp$Group)