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Save Individual HMM State Plots to Disk

Source: R/HmmSinglePlot.R
HMMSinglePlot.Rd

Generates and saves individual plots of HMM-inferred sleep states to PNG files. Creates one plot per individual per day, organized in a directory structure by genotype. Each plot shows the time-series of state assignments with a light/dark phase annotation.

Note: This function is designed for batch processing and automatically saves plots to disk. It does not return plots for interactive viewing. For interactive plotting, use HMMplot or HMMFacetedPlot.

Usage

HMMSinglePlot(HMMinferList, col_palette = "default")

Arguments

HMMinferList

A list, typically the output from HMMbehavr. The second element (HMMinferList[[2]]) must be a data frame with the VITERBIDecodedProfile containing: ID, day, timestamp, state_name, and genotype.

col_palette

Character string specifying the color palette. Options:

"default"

Standard FlyDreamR colors

"AG"

Alternative palette

Default: "default".

Value

NULL. This function is called for its side effect of saving plot files to disk. It does not return plot objects.

Details

File Organization

Plots are saved with the following structure:


./profiles_all/
  └── [Genotype]/
      ├── [ID]_day1_4states.png
      ├── [ID]_day2_4states.png
      └── ...

## File Naming Each file is named: [ID]_day[N]_4states.png

  • ID is sanitized (timestamps and pipe characters removed)

  • Day number is appended

  • Suffix "_4states" indicates 4-state HMM

Directory Creation

The function automatically creates necessary directories:

  • Base directory: ./profiles_all/

  • Subdirectories for each unique genotype

Error Handling

  • If state separation fails for an individual-day, that plot is skipped silently (wrapped in tryCatch)

  • If directory creation fails, file save is skipped

  • Progress is printed to console for each file

Performance

For large datasets:

  • 32 individuals × 3 days = 96 PNG files

  • Approximate time: 30-60 seconds

  • Disk space: ~100-200 KB per plot

Note

This function is most useful for:

  • Creating archival records of individual results

  • Manual inspection of individual flies

  • Sharing results with collaborators

  • Supplementary materials for publications

For interactive analysis or presentation figures, consider using HMMplot or HMMFacetedPlot instead, which return ggplot objects that can be customized and viewed interactively.

See also

HMMplot for interactive tile plot HMMFacetedPlot for interactive faceted plot HMMbehavr for generating input data

Examples

if (FALSE) { # \dontrun{
# Generate HMM results
hmm_results <- HMMbehavr(processed_data)

# Save all plots with default colors
HMMSinglePlot(hmm_results)

# Save with alternative palette
HMMSinglePlot(hmm_results, col_palette = "AG")

# Check output directory structure
list.dirs("./profiles_all", recursive = TRUE)

# List all generated files
list.files("./profiles_all",
           pattern = "\\.png$",
           recursive = TRUE)
} # }