Plot Gene Detector Volcano

This function plots a volcano plot for gene detection using GeneDiscoveR.

plot_genediscover_detector_volcano(
  GeneDiscoveRobject = NULL,
  annotationTable = NULL,
  name = NULL,
  title = "",
  type = "TPStype",
  categories = c("Diterpene", "Bacterial", "Fungi")
)

Arguments

GeneDiscoveRobject: The GeneDiscoveR object containing the gene detection results.
annotationTable: The annotation table used for filtering genes based on categories. With OG, Gene Tree Parent Clade, GeneID and type columns.
name: The name of the gene detection result to plot.
title: The title of the volcano plot.
type: The type of genes to plot (default is "TPStype"). Is the column name in the annotationTable.
categories: The categories of genes to include in the plot (default is c("Diterpene", "Bacterial", "Fungi")).

Value

A ggplot object representing the volcano 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)

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

# Select species by phenotype
GeneDiscoveRobject <- select_species_by_phenotype(GeneDiscoveRobject = GeneDiscoveRobject, columnPhenotype = "Oil-body-type", columnID = "OrthofinderID", type = "one_in_specialized_cell")
GeneDiscoveRobject <- select_species_by_phenotype(GeneDiscoveRobject = GeneDiscoveRobject, columnPhenotype = "Oil-body-type", columnID = "OrthofinderID", type = "many_in_all_cells")

# Gene identification by phenotype
GeneDiscoveRobject <- gene_identification_by_phenotype(GeneDiscoveRobject = GeneDiscoveRobject, formula = as.formula("many_in_all_cells ~ one_in_specialized_cell"), statistic = "Fisher", name = "PerType", cores = 8)

library(readr)

# Load the TPS genes
TPSgenes <- read_tsv(system.file("extdata", "TPSgenes.tsv", package = "GeneDiscoveR"), col_names = TRUE)
#> Rows: 365 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (8): Species, Ndna, OrthofinderID, GeneID, collapseID, TPStype, OG, Gene...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
TPScategories <- c("Diterpene", "Bacterial", "Fungi")
title <- "Fisher's Exact Test per Type of Oil-body with TPS genes"
plot_genediscover_detector_volcano(GeneDiscoveRobject, annotationTable = TPSgenes, title = title, name = "PerType", type = "TPStype", categories = TPScategories)

# Volcano plot with TPS genes

# Output: A ggplot object representing the volcano plot.

Arguments

Value

See also

Examples