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Produce volcano plots to display miRNA/gene differential expression

Source: R/visualization.R
plotVolcano.Rd

This function allows the user to create publication-quality volcano plots to represent the results of miRNA/gene differential expression. In this kind of plots, the x-axis is relative to the log2 fold change between biological conditions, while the y-axis contains the negative base-10 logarithm of the p-value. Note, that even if volcano plots display unadjusted p-values on the y-axis, the cutoff level shown in this plot derive from the adjusted p-value cutoff used for differential expression analysis.

Usage

plotVolcano(
  mirnaObj,
  assay,
  labels = NULL,
  boxedLabel = TRUE,
  pointSize = 3,
  pointAlpha = 0.4,
  interceptWidth = 0.6,
  interceptColor = "black",
  interceptType = "dashed",
  colorScale = c("blue", "grey", "red"),
  title = NULL,
  fontSize = 12,
  fontFamily = "",
  legend = "none",
  borderWidth = 1,
  allBorders = TRUE,
  grid = FALSE
)

Arguments

mirnaObj

A MirnaExperiment object containing miRNA and gene data

assay

The results to display. It must be either 'microRNA', to plot miRNA differential expression, or 'genes', to show the results for genes

labels

The labels to show on the graph. Default is NULL not to include labels. This parameter can be a character vector containing the IDs of the features that you want to display. Alternatively, this parameter can also be the number of most significant features for which we want to plot labels

boxedLabel

Logical, whether to show labels inside a rectangular shape (default) or just as text elements

pointSize

The size of points in the volcano plot (default is 3)

pointAlpha

The transparency of points in the volcano plot (default is 0.4)

interceptWidth

The width of cutoff intercepts (default is 0.6)

interceptColor

It must be an R color name that specifies the color of cutoff intercepts. Default is black. Available color formats include color names, such as 'blue' and 'red', and hexadecimal colors specified as #RRGGBB

interceptType

It specifies the line type used for cutoff intercepts. It must be either 'blank', 'solid', 'dashed' (default), 'dotted', 'dotdash', 'longdash' or 'twodash'

colorScale

It must be a character vector of length 3 containing valid R color names for downregulated, non significant, and upregulated features, respectively. Default value is c('blue', 'grey', 'red'). Available color formats include color names, such as 'blue' and 'red', and hexadecimal colors specified as #RRGGBB

title

The title of the plot. Default is NULL not to include a plot title

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 none so that 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 TRUE

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 volcano plot for genes
plotVolcano(obj, "genes")