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Dot plot of -log10(p-value) for log2 fold-change comparisons along chromosomes

Source: R/ttest_scatter.R
ttest_scatter.Rd

For each chromosome, runs a Welch t-test on log2 fold-change values ("Autosome vs Autosomes" and "X vs Autosomes") and displays results as a dot plot.

Usage

ttest_scatter(
  object = NULL,
  title = NULL,
  subtitle = NULL,
  ylab = "-log10(p-value)",
  fc_col = "Fold",
  chr_col = "seqnames",
  autosomes = c("chrI", "chrII", "chrIII", "chrIV", "chrV"),
  chr_X = "chrX",
  chr_colors = c(chrI = "#66C2A5", chrII = "#FC8D62", chrIII = "#8DA0CB", chrIV =
    "#E78AC3", chrV = "#A6D854", chrX = "#EF9A9A"),
  pvalue_threshold_y = -log10(0.05),
  pvalue_y_position_offset = 0.5,
  pvalue_x_position = 6,
  output_pdf = NULL,
  pdf_width = 8,
  pdf_height = 6
)

Arguments

object

A data.frame or tibble.

title

Character. Main plot title. Default NULL.

subtitle

Character. Plot subtitle. Default NULL.

ylab

Character. Y-axis label. Default "-log10(p-value)".

fc_col

Character. Column name for log2 fold-change. Default "Fold".

chr_col

Character. Chromosome column name. Default "seqnames".

autosomes

Character vector. Autosome names.

chr_X

Character. Sex chromosome name. Default "chrX".

chr_colors

Named character vector. Colors per chromosome.

pvalue_threshold_y

Numeric. Significance threshold on -log10 scale. Default -log10(0.05).

pvalue_y_position_offset

Numeric. Vertical offset (in plot units) for placing the p-value threshold label above the horizontal reference line. Default: 0.5.

pvalue_x_position

Numeric. Absolute X position (in plot units) for p-value threshold label, right of the plot. Default 6.

output_pdf

Character. Optional PDF output path. Default NULL.

pdf_width

Numeric. Default 8.

pdf_height

Numeric. Default 6.

Value

A named list with plot and results.

Examples

if (FALSE) { # \dontrun{
res <- ttest_scatter(
  object = my_peaks,
  title  = "FC t-test (Autosome vs Autosomes and X vs Autosomes)"
)
res$plot
} # }