plotTwoFactor: Bar plot of gene expression for two-factor experiments

In rtpcr: qPCR Data Analysis

Bar plot of gene expression for two-factor experiments

Description

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

Usage

plotTwoFactor(
  data,
  x_col,
  y_col,
  group_col,
  Lower.se_col,
  Upper.se_col,
  letters_col = NULL,
  letters_d = 0.2,
  dodge_width = 0.8,
  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).
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 plotTwoFactor function generates a bar plot of average fold change (relative expression) values for target genes using expression tables produced by functions such as ANOVA_DDCt() or ANOVA_DCt(). One factor is mapped to the x-axis and the second factor is used to group the bars (fill aesthetic). Error bars represent standard error (SE) or 95% confidence intervals (CI). Optional grouping letters from post hoc statistical comparisons can be displayed.

Value

A ggplot object

Author(s)

Ghader Mirzaghaderi

Examples

a <- ANOVA_DCt(data_2factorBlock, block = "Block", numberOfrefGenes = 1)
data <- a$Results

p1 <- plotTwoFactor(
  data = data,
  x_col = 2,
  y_col = 3,
  group_col = 1,
  Lower.se_col = 8,
  Upper.se_col = 9,
  letters_col = 12,
  letters_d = 0.2,
  fill_colors = c("aquamarine4", "gold2"),
  alpha = 1,
  col_width = 0.7,
  dodge_width = 0.7,
  base_size = 16, 
  legend_position = c(0.2, 0.8)
)
p1


p2 <- plotTwoFactor(
  data = data,
  x_col = 2,
  y_col = 4,
  group_col = 1,
  Lower.se_col = 10,
  Upper.se_col = 11,
  letters_col = 12,
  letters_d = 0.2,
  fill_colors = c("aquamarine4", "gold2"),
  alpha = 1,
  col_width = 0.7,
  dodge_width = 0.7,
  base_size = 16, 
  legend_position = c(0.2, 0.8)
)
p2

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