Represent differentially expressed miRNAs/genes as boxplots, barplots or violinplots

This function is able to produce boxplots, barplots and violinplots that are useful to visualize miRNA and gene differential expression. The user just has to provide a vector of interesting miRNA/genes that he wants to plot (e.g. "hsa-miR-34a-5p", "hsa-miR-146b-5p", "PAX8"). The chart type can be specified through the graph parameter.

Usage

plotDE(
  mirnaObj,
  features,
  condition = NULL,
  graph = "boxplot",
  linear = TRUE,
  showSignificance = TRUE,
  starSig = TRUE,
  pCol = "adj.P.Val",
  sigLabelSize = 7,
  digits = 3,
  nameAsTitle = FALSE,
  colorScale = NULL,
  fontSize = 12,
  fontFamily = "",
  legend = "top",
  borderWidth = 1,
  allBorders = FALSE,
  grid = FALSE
)

Arguments

mirnaObj: A MirnaExperiment object containing miRNA and gene data
features: A character vector containing the genes/miRNAs to plot
condition: It must be NULL (default) to plot expression based on the group variable used for differential expression analysis. Alternatively, it must be a character/factor object that specifies group memberships (eg. c("healthy, "healthy", "disease", "disease"))
graph: The type of plot to produce. It must be one of boxplot (default), barplot, violinplot
linear: Logical, whether to plot expression levels in linear scale or in log2 space. Default is TRUE in order to use the linear space
showSignificance: Logical, whether to display statistical significance or not. Default is TRUE
starSig: Logical, whether to represent statistical significance through stars. Default is TRUE, and the significance scale is: * for \(p < 0.05\), ** for \(p < 0.01\), *** for \(p < 0.001\), and **** for \(p < 0.0001\). If starSig is set to FALSE, p-values or adjusted p-values will be reported on the plot as numbers
pCol: The statistics used to evaluate comparison significance. It must be one of P.Value, to use unadjusted p-values, and adj.P.Val (default), to use p-values corrected for multiple testing
sigLabelSize: The size for the labels used to show statistical significance. Default is 7, which is well suited for representing p-values as significance stars. However, if starSig is set to FALSE, the user might have to downsize this parameter
digits: The number of digits to show when p-values are reported as numbers (when starSig is FALSE). Default is 3
nameAsTitle: Logical, if set to TRUE, the miRNA/gene name will be added as plot title, and the x-axis and legend will be removed. Note that this option is only considered if features contains just one miRNA/gene. Default is FALSE
colorScale: It must be a named character vector where values correspond to R colors, while names coincide with the groups specified in the condition parameter (eg. c("healthy" = "green", "disease" = "red")). Default is NULL, in order to use the default color scale. Available color formats include color names, such as 'blue' and 'red', and hexadecimal colors specified as #RRGGBB
fontSize: The base size for text elements within the plot. Default is 12
fontFamily: The base family for text elements within the plot
legend: The position of the legend. Allowed values are top, bottom, right, left and none. The default setting is top to show a legend above the plot. If none is specified, the legend will not be included in the graph.
borderWidth: The width of plot borders (default is 1)
allBorders: Logical, whetether to show all panel borders, or just the bottom and left borders. Default is FALSE
grid: Logical, whether to show grid lines or not. Default is FALSE

Value

An object of class ggplot containing the plot.

Author

Jacopo Ronchi, jacopo.ronchi@unimib.it

Examples

# load example MirnaExperiment object
obj <- loadExamples()

# produce a boxplot for PAX8 and miR-34a-5p
plotDE(obj, features = c("hsa-miR-34a-5p", "PAX8"))