Bar plot of single gene expression (Delta Delta Ct method)

Creates a bar plot of relative gene expression (fold change) values from single gene analysis

Usage

plotSingleGene(
  res,
  col_width = 0.8,
  err_width = 0.15,
  color = "black",
  alpha = 1,
  base_size = 12,
  d = 0.4,
  ...
)

Arguments

res

An object created by the ANOVA_DDCt() function

col_width

Numeric. Width of bars (default 0.8)

err_width

Numeric. Width of error bars (default 0.15)

color

Optional color for the bar outline

alpha

Numeric. Transparency of bars (default 1)

base_size

Numeric. Base font size for theme (default 12)

d

Distance between horizontal significance lines

...

Additional ggplot2 layer arguments

Value

A bar plot of Delta Delta Ct showing pairwise significance

Examples

res <- ANOVA_DDCt(
data_2factor,
numOfFactors = 2,
specs = "Drought",
numberOfrefGenes = 1,
block = NULL,
analyseAllTarget = TRUE) # If you have multi-target gene data, specify a single target gene.
#> 
#> Relative Expression
#>   gene contrast     ddCt      RE     LCL     UCL   log2FC      se Lower.se.RE
#> 1   PO       D0  0.00000 1.00000 0.00000 0.00000  0.00000 0.09564     0.93586
#> 2   PO D1 vs D0 -0.09833 1.07054 0.75825 1.51143 -0.09833 0.22675     0.91483
#> 3   PO D2 vs D0 -1.84667 3.59668 2.54751 5.07795 -1.84667 0.04497     3.48630
#>   Upper.se.RE Lower.se.log2FC Upper.se.log2FC p.value sig
#> 1     1.06854        -0.09564         0.09564  1.0000    
#> 2     1.25274        -0.12842         0.32508  0.6744    
#> 3     3.71056         1.80170         1.89164  0.0000 ***
#> 
#> The D0 level was used as calibrator.
#> Note: Using default model for statistical analysis: wDCt ~ Drought * Genotype 

plotSingleGene(res, fill = "cyan4", color = "black", base_size = 12)