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Re-analyze and edit saved charisma objects

Source: R/charisma2.R
charisma2.Rd

The charisma2 function allows users to step through and edit previously saved charisma objects. This function enables rewinding to specific merge or replacement states, applying different thresholds, or continuing interactive editing from any saved state, ensuring full reproducibility of the analysis.

Usage

charisma2(
  charisma.obj,
  interactive = TRUE,
  new.threshold = NULL,
  which.state = c("none", "merge", "replace"),
  state.index = NULL,
  k.override = NULL
)

Arguments

charisma.obj

A charisma object to be re-analyzed. Cannot be a charisma2 object (attempting to run charisma2 on a charisma2 object will produce an error).

interactive

Logical. If TRUE, enters interactive mode for manual color adjustments. Default is TRUE.

new.threshold

Numeric value between 0 and 1 to apply a different color proportion threshold than the original analysis. If NULL, uses the original threshold. Default is NULL.

which.state

Character string specifying which state to revert to. Options are "none" (most recent state), "merge" (specific merge state), or "replace" (specific replacement state). Default is "none".

state.index

Integer specifying which state index to revert to when which.state is "merge" or "replace". Must be provided if which.state is not "none". Default is NULL.

k.override

Integer to force a specific number of color clusters. Default is NULL.

Value

A charisma2 object (also of class charisma) containing the same structure as a charisma object, with updated states based on the specified reversion point and any new operations performed.

Details

The charisma2 function provides powerful state management capabilities:

  • State rewinding: Jump to any previous merge or replacement state

  • Re-thresholding: Apply different color proportion thresholds without re-running the entire pipeline

  • Continued editing: Resume interactive editing from saved states

  • Full provenance: All operations maintain complete history for reproducibility

Note: Interactive adjustment of merge states is disabled if replacement states exist, as replacement operations depend on post-merge cluster indices.

References

Schwartz, S.T., Tsai, W.L.E., Karan, E.A., Juhn, M.S., Shultz, A.J., McCormack, J.E., Smith, T.B., and Alfaro, M.E. (2025). charisma: An R package to perform reproducible color characterization of digital images for biological studies. (In Review).

See also

charisma for initial color classification, plot.charisma for visualization

Examples

# Load a previously saved charisma object
obj <- system.file("extdata", "Tangara_fastuosa.RDS", package = "charisma")
obj <- readRDS(obj)

if (FALSE) { # \dontrun{
# Examples that require objects with merge/replacement states
# (These examples show the syntax but won't run with the provided test data)

# Revert to a specific merge state (if merge states exist)
if (length(obj$merge_states) >= 2) {
  result <- charisma2(obj, which.state = "merge", state.index = 2)
}

# Revert to a specific replacement state (if replacement states exist)
if (length(obj$replacement_states) >= 1) {
  result <- charisma2(obj, which.state = "replace", state.index = 1)
}

# Re-enter interactive mode with original threshold
obj <- system.file("extdata", "Tangara_fastuosa.RDS", package = "charisma")
obj <- readRDS(obj)
result <- charisma2(obj, interactive = TRUE)
} # }