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Visualization of differential expression in a volcano plot

Source: R/plotFunctions.R
plotDiffExp.Rd

This function plots differentially expressed repertoire levels calculated using the diffExpGroup in a volcano plot.

Usage

plotDiffExp(
  x,
  level = c("aaClone", "ntClone", "V", "J", "VJ", "ntCDR3", "aaCDR3"),
  group = c("cell_subset", "amTreg", "nTreg"),
  FC.TH = 2,
  PV.TH = 0.05,
  top = 10
)

Arguments

x

an object of class RepSeqExperiment

level

a character specifying the level of the repertoire on which the diversity should be estimated. Should be one of "aaClone","ntClone", "V", "J", "VJ", "ntCDR3" or "aaCDR3".

group

a vector of character indicating the column name in the mData slot, as well as the two groups to be compared.

FC.TH

an integer indicating the log2FoldChange threshold. Default is 2.

PV.TH

an integer indicating the adjusted pvalue threshold. Default is 0.05.

top

an integer indicating the top n significant labels to be shown on the volcano plot. Default is 10.

Examples


plotDiffExp(x = RepSeqData,
            level = "V",
            group = c("cell_subset", "amTreg", "nTreg"),
            top = 10,
            FC.TH = 1,
            PV.TH = 0.05)
#> Warning: some variables in design formula are characters, converting to factors
#> using pre-existing size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing
#> Warning: Removed 8 rows containing missing values or values outside the scale range
#> (`geom_text_repel()`).