pcvr (version 1.2.0)

bw.time: Time conversion and plotting for bellwether data

Description

Time conversion and plotting for bellwether data

Usage

bw.time(
  df = NULL,
  mode = c("DAS", "DAP", "DAE"),
  plantingDelay = NULL,
  phenotype = NULL,
  cutoff = 1,
  timeCol = "timestamp",
  group = "Barcodes",
  plot = TRUE,
  format = "%Y-%m-%d %H:%M:%S",
  traitCol = "trait",
  valueCol = "value",
  index = NULL,
  digits = 0
)

Value

The input dataframe with new numeric columns for different ways of describing time in the experiment. If plot is TRUE then a ggplot is also returned as part of a list.

Arguments

df

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

mode

One of "DAS", "DAP" or "DAE" (Days After Planting and Days After Emergence). Defaults to adding all columns. Note that if timeCol is not numeric then DAS is always returned.

plantingDelay

If `mode` includes "DAP" then `plantingDelay` is used to adjust "DAS"

phenotype

If `mode` includes "DAE" then this is the phenotype used to classify emergence.

cutoff

If `mode` includes "DAE" then this value is used to classify emergence. Defaults to 1, meaning an image with a value of 1 or more for `phenotype` has "emerged".

timeCol

Column of input time values, defaults to "timestamp". If this is not numeric then it is assumed to be a timestamp in the format of the format argument.

group

Grouping variables to specify unique plants as a character vector. This defaults to "Barcodes". These taken together should identify a unique plant across time, although often "angle" or "rotation" should be added.

plot

Logical, should plots of the new time variables be printed?

format

An R POSIXct format, defaults to lemnatech standard format. This is only used if timeCol is not a numeric.

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.

index

Optionally a time to use as the beginning of the experiment. This may be useful if you have multiple datasets or you are adding data from bw.water and plants were watered before being imaged or if you want to index days off of midnight. This defaults to NULL but will take any value coercible to POSIXct by as.POSIXct(... , tz="UTC") such as "2020-01-01 18:30:00"

digits

Number of digits to round DAS to if timeCol is not numeric, defaults to 0.

Examples

# \donttest{
f <- "https://raw.githubusercontent.com/joshqsumner/pcvrTestData/main/pcv4-single-value-traits.csv"
tryCatch(
  {
    sv <- read.pcv(
      f,
      mode = "wide", 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 = FALSE
    )

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