plotThreeFactor: Bar plot of gene expression for three-factor experiments

In rtpcr: qPCR Data Analysis

Bar plot of gene expression for three-factor experiments

Description

Creates a bar plot of relative gene expression (fold change) values from a three-factor experiment, including error bars and statistical significance annotations.

Usage

plotThreeFactor(
  data,
  x_col,
  y_col,
  group_col,
  facet_col,
  Lower.se_col,
  Upper.se_col,
  letters_col = NULL,
  letters_d = 0.2,
  dodge_width = 0.9,
  col_width = 0.8,
  err_width = 0.15,
  fill_colors = NULL,
  alpha = 1,
  base_size = 12,
  legend_position = "right",
  ...
)

Arguments

data	A data frame containing expression results, typically obtained from ANOVA_DDCt() or ANOVA_DCt().
x_col	Integer specifying the column number used for the x-axis factor.
y_col	Integer specifying the column number used for the bar height (relative expression or fold change).
group_col	Integer specifying the column number used for grouping bars (fill aesthetic).
facet_col	Integer specifying the column number used for faceting the plot.
Lower.se_col	Integer specifying the column number used for the lower limit of the error bar.
Upper.se_col	Integer specifying the column number used for the upper limit of the error bar.
letters_col	Integer specifying the column number containing grouping letters from statistical comparisons.
letters_d	Numeric specifying the distance between sig letters and error bar.
dodge_width	Numeric. Width of the dodge position adjustment for grouped bars.
col_width	Numeric. Width of bars (default 0.8)
err_width	Numeric. Width of error bars (default 0.15)
fill_colors	Optional vector of fill colors
alpha	Numeric. Transparency of bars (default 1)
base_size	Numeric. Base font size (default 12)
legend_position	Character or numeric vector. Position of legend (default "right")
...	Additional ggplot2 layer arguments (e.g., fill, alpha, color)

Details

The plotThreeFactor function generates a bar plot of average fold change (relative expression) values for target genes using the output expression tables produced by functions such as ANOVA_DDCt() or ANOVA_DCt(). One factor is mapped to the x-axis, one to bar grouping (fill), and one to faceting. Error bars represent standard error (SE) or 95% confidence intervals, and optional grouping letters from post hoc statistical comparisons can be displayed.

Value

A ggplot object

Author(s)

Ghader Mirzaghaderi

Examples

# Perform analysis first
res <- ANOVA_DCt(
  data_3factor,
  numberOfrefGenes = 1,
  block = NULL
)

data <- res$Result

# Generate three-factor bar plot
p <- plotThreeFactor(
  data,
  x_col = 3,        # x-axis factor
  y_col = 5,        # bar height
  group_col = 1,    # grouping (fill)
  facet_col = 2,    # faceting factor
  Lower.se_col = 11,
  Upper.se_col = 12,
  letters_col = 13,
  letters_d = 0.3,
  col_width = 0.7, 
  dodge_width = 0.7,# controls spacing
  fill_colors = c("blue", "brown"),
  base_size = 16, 
  alpha = 1,
  legend_position = c(0.1, 0.2)
)

library(ggplot2)
p + theme(
  panel.border = element_rect(color = "black", fill = NA, linewidth = 0.5)
)

rtpcr documentation built on Dec. 19, 2025, 5:07 p.m.