Bar plot of the relative gene expression (\(\Delta C_T\) method) from the qpcrANOVARE output of a single-factor experiment data

Bar plot of the relative expression of a gene along with the standard error (se), 95% confidence interval (ci) and significance. oneFACTORplot is mainly useful for a one-factor experiment with more than two levels.

oneFACTORplot(
  res,
  width = 0.4,
  fill = "skyblue",
  y.axis.adjust = 0.5,
  y.axis.by = 2,
  errorbar,
  show.letters = TRUE,
  letter.position.adjust = 0.1,
  ylab = "Relative Expression",
  xlab = "none",
  fontsize = 12,
  fontsizePvalue = 5,
  axis.text.x.angle = 0,
  axis.text.x.hjust = 0.5
)

Arguments

res

an FC data frame object created by qpcrANOVARE(x)$Result function on a one factor data such as data_1factor.

width

a positive number determining bar width.

fill

specify a fill color.

y.axis.adjust

a negative or positive number for reducing or increasing the length of the y axis.

y.axis.by

determines y axis step length.

errorbar

Type of error bar, can be se or ci.

show.letters

a logical variable. If TRUE, mean grouping letters are added to the bars.

letter.position.adjust

adjust the distance between the grouping letters to the error bars.

ylab

the title of the y axis.

xlab

the title of the x axis.

fontsize

size of all fonts of the plot.

fontsizePvalue

font size of the pvalue labels

axis.text.x.angle

angle of x axis text

axis.text.x.hjust

horizontal justification of x axis text

Value

Bar plot of the average fold change for target genes along with the significance and the standard error or 95% confidence interval as error bars.

Details

The oneFACTORplot function generates the bar plot of the average fold change for target genes along with the significance and the 95% confidence interval as error bars.

Author

Ghader Mirzaghaderi

Examples

# Before plotting, the result needs to be extracted as below:
res <- qpcrANOVARE(data_1factor, numberOfrefGenes = 1, block = NULL)$Result
#> Analysis of Variance Table
#> 
#> Response: wDCt
#>           Df Sum Sq Mean Sq F value   Pr(>F)   
#> T          2 4.9393 2.46963  12.345 0.007473 **
#> Residuals  6 1.2003 0.20006                    
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#> 
#> Relative expression table
#>   SA     RE    LCL    UCL     se Lower.se Upper.se letters
#> 1 L3 0.9885 0.6379 1.5318 0.0841   0.9325   1.0478      a 
#> 2 L2 0.6271 0.4047 0.9717 0.4388   0.4626   0.8500      a 
#> 3 L1 0.2852 0.1840 0.4419 0.0208   0.2811   0.2893       b

# Bar plot
oneFACTORplot(res,
         width = 0.4,
         fill = "skyblue",
         y.axis.adjust = 1,
         y.axis.by = 0.2,
         errorbar = "se",
         show.letters = TRUE,
         letter.position.adjust = 0.05,
         ylab = "Relative Expression",
         xlab = "Factor Levels",
         fontsize = 12)