pcvr (version 1.2.0)

cumulativePheno: Reduce phenotypes in longitudinal data to cumulative sums of phenotypes.

Description

Often in bellwether experiments we are curious about the effect of some treatment vs control. For certain routes in analysing the data this requires considering phenotypes as relative differences compared to a control.

Usage

cumulativePheno(
  df,
  phenotypes = NULL,
  group = "barcode",
  timeCol = "DAS",
  traitCol = "trait",
  valueCol = "value"
)

Value

A dataframe with cumulative sum columns added for specified phenotypes

Arguments

df

Dataframe to use, this can be in long or wide format.

phenotypes

A character vector of column names for the phenotypes that should be compared against control.

group

A character vector of column names that identify groups in the data. Defaults to "barcode". These groups will be calibrated separately, with the exception of the group that identifies a control within the greater hierarchy.

timeCol

Column name to use for time data.

traitCol

Column with phenotype names, defaults to "trait". This should generally not need to be changed from the default. If this and valueCol are present in colnames(df) then the data is assumed to be in long format.

valueCol

Column with phenotype values, defaults to "value". This should generally not need to be changed from the default.

Examples

# \donttest{
f <- "https://raw.githubusercontent.com/joshqsumner/pcvrTestData/main/pcv4-single-value-traits.csv"
tryCatch(
  {
    sv <- read.pcv(
      f,
      reader = "fread"
    )
    sv$genotype <- substr(sv$barcode, 3, 5)
    sv$genotype <- ifelse(sv$genotype == "002", "B73",
      ifelse(sv$genotype == "003", "W605S",
        ifelse(sv$genotype == "004", "MM", "Mo17")
      )
    )
    sv$fertilizer <- substr(sv$barcode, 8, 8)
    sv$fertilizer <- ifelse(sv$fertilizer == "A", "100",
      ifelse(sv$fertilizer == "B", "50", "0")
    )

    sv <- bw.time(sv,
      plantingDelay = 0, phenotype = "area_pixels", cutoff = 10,
      timeCol = "timestamp", group = c("barcode", "rotation"), plot = TRUE
    )$data
    sv <- bw.outliers(sv,
      phenotype = "area_pixels", group = c("DAS", "genotype", "fertilizer"),
      plotgroup = c("barcode", "rotation")
    )$data
    phenotypes <- colnames(sv)[19:35]
    phenoForm <- paste0("cbind(", paste0(phenotypes, collapse = ", "), ")")
    groupForm <- "DAS+DAP+barcode+genotype+fertilizer"
    form <- as.formula(paste0(phenoForm, "~", groupForm))
    sv <- aggregate(form, data = sv, mean, na.rm = TRUE)
    pixels_per_cmsq <- 42.5^2 # pixel per cm^2
    sv$area_cm2 <- sv$area_pixels / pixels_per_cmsq
    sv$height_cm <- sv$height_pixels / 42.5
    df <- sv
    phenotypes <- c("area_cm2", "height_cm")
    group <- c("barcode")
    timeCol <- "DAS"
    df <- cumulativePheno(df, phenotypes, group, timeCol)


    sv_l <- read.pcv(
      f,
      mode = "long", reader = "fread"
    )
    sv_l$genotype <- substr(sv_l$barcode, 3, 5)
    sv_l$genotype <- ifelse(sv_l$genotype == "002", "B73",
      ifelse(sv_l$genotype == "003", "W605S",
        ifelse(sv_l$genotype == "004", "MM", "Mo17")
      )
    )
    sv_l$fertilizer <- substr(sv_l$barcode, 8, 8)
    sv_l$fertilizer <- ifelse(sv_l$fertilizer == "A", "100",
      ifelse(sv_l$fertilizer == "B", "50", "0")
    )
    sv_l <- bw.time(sv_l,
      plantingDelay = 0, phenotype = "area_pixels", cutoff = 10,
      timeCol = "timestamp", group = c("barcode", "rotation")
    )$data
    sv_l <- cumulativePheno(sv_l,
      phenotypes = c("area_pixels", "height_pixels"),
      group = c("barcode", "rotation"), timeCol = "DAS"
    )
  },
  error = function(e) {
    message(e)
  }
)
# }