Plot OGs and HOGs per inflation

This function plots the number of orthogroups (OGs) and hierarchical orthogroups (HOGs) per inflation. If a run is active, a vertical dashed line is added to the plot on the active run's inflation value. The function is only for executions with multiple inflation values.

plot_OGs_HOGs_per_inflation(GeneDiscoveRobject = NULL)

Arguments

GeneDiscoveRobject

An object of class GeneDiscoveR. Default is NULL.

Value

An object of class "ggplot" representing the plot.

Examples

# Create a GeneDiscoveR object
N0sDir <- system.file("extdata", "N0-1dot3-6", package = "GeneDiscoveR")
overallsDir <- system.file("extdata", "Comparatives-1dot3-6", package = "GeneDiscoveR")
dataFile <- system.file("extdata", "annotatedCDSs.tsv", package = "GeneDiscoveR")
minInflation <- 1.3
maxInflation <- 6
stepInflation <- 0.1

GeneDiscoveRobject <- GeneDiscoveR(overallsDir = overallsDir, N0sDir = N0sDir, dataFile = dataFile, minInflation = minInflation, maxInflation = maxInflation, stepInflation = stepInflation)

# Calculate median statistics

GeneDiscoveRobject <- calculate_median_statistics(GeneDiscoveRobject, cores = 8)

# Plot number of orthogroups (OGs) and hierarchical orthogroups (HOGs) per inflation
plot_OGs_HOGs_per_inflation(GeneDiscoveRobject)


# Plot number of orthogroups (OGs) and hierarchical orthogroups (HOGs) per inflation with active run

GeneDiscoveRobject <- set_run_active(GeneDiscoveRobject, InflationValue = 1.8)
#> -----------From OrthoFinder-----------
#> The process has been completed successfully
plot_OGs_HOGs_per_inflation(GeneDiscoveRobject)