plotOneFactor: Bar plot of gene expression for single-factor experiments

In rtpcr: qPCR Data Analysis

Bar plot of gene expression for single-factor experiments

Description

Creates a bar plot of relative gene expression (fold change) values from a single-factor experiment, including standard error or confidence interval error bars and statistical significance.

Usage

plotOneFactor(
  data,
  x_col,
  y_col,
  Lower.se_col,
  Upper.se_col,
  letters_col = NULL,
  letters_d = 0.2,
  col_width = 0.8,
  err_width = 0.15,
  fill_colors = "grey40",
  alpha = 1,
  base_size = 12,
  legend_position = "none",
  ...
)

Arguments

data	Data frame
x_col	Numeric. Column index for x-axis
y_col	Numeric. Column index for bar height
Lower.se_col	Numeric. Column index for lower SE
Upper.se_col	Numeric. Column index for upper SE
letters_col	Optional column index for grouping letters
letters_d	Numeric. Vertical offset for letters (default 0.2)
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 for theme (default 12)
legend_position	Character. Legend position (default "right")
...	Additional valid ggplot2 layer arguments

Details

The plotOneFactor function generates a bar plot of fold change values for target genes using the output expression tables produced by functions such as ANOVA_DDCt() or ANOVA_DCt(). Error bars can represent either standard error (SE) or 95% confidence intervals, and optional grouping letters from post hoc statistical comparisons can be displayed above the bars.

Value

ggplot2 plot object

Author(s)

Ghader Mirzaghaderi

Examples

a <- ANOVA_DCt(
data_1factor,
numberOfrefGenes = 1,
block = NULL
)
data <- a$Results

plotOneFactor(
  data,
  x_col = 1,
  y_col = 2,
  Lower.se_col = 7,
  Upper.se_col = 8,
  letters_col = 11,
  letters_d = 0.1,
  col_width = 0.7,
  err_width = 0.15,
  fill_colors = "skyblue",
  alpha = 1,
  base_size = 16
)

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