replotCumulSpeSimulAggregated: Plot a figure based on the data.frame created by the...
In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

replotCumulSpeSimulAggregated

R Documentation

Plot a figure based on the data.frame created by the cumulSpe-like function

Description

Plot a figure based on the data.frame created by the cumulSpe-like function

Usage

replotCumulSpeSimulAggregated(DF_long, cor1, reference, Title,
  CorrelationPlot = TRUE, relabel = TRUE, cor2, simul1,
  aggregateBool = TRUE, aggregMethod = "rowMeans",
  labelVec = setNames(c("Protein/mRNA pairs",
  "mRNA/mRNA pairs ('ideal' reference)", "Randomised Protein/mRNA pairs"),
  c("Cor", "reference", "Simul")), sizeLine = 1, palette,
  legendText = 0.92, base_family = "Linux Libertine", base_size = 11,
  centerTitle = TRUE, out = "plot", VinterO8 = FALSE)

Arguments

`DF_long`	data.frame in a long format
`cor1`	named numeric vector that comprises the correlation between two studies.
`reference`	named numeric vector that comprises the correlation between two (transcriptomic) studies that can be used as a reference
`Title`	character string. Title of the plot.
`CorrelationPlot`	boolean. Default:TRUE. Whether to add the correlation plot to help for the interpretation.
`relabel`	boolean. Default: TRUE. Whether the categories should be relaballed with the content of labelVec
`cor2`	named numeric vector that comprises the correlation between two studies.
`simul1`	named numeric vector that comprises the result of the random permutations on cor1
`aggregateBool`	boolean. Default: TRUE. Whether to aggregate all the simulation of a given comparison together.
`aggregMethod`	character string for the name of the method to aggregate the different simulation together. Default: 'rowMeans'
`labelVec`	named character string that allows to name the different categories to be displayed in the legend. The names should be 'cor1, 'ref', 'simul1', .... and the content the labels Default: "setNames(c("Protein/mRNA pairs", "mRNA/mRNA pairs ('ideal' reference)", "Randomised Protein/mRNA pairs"), c('Cor','reference','simul1'))"
`sizeLine`	positive numeric. Size of the lines of the plot
`palette`	named vector of character strings. Allows to customise the colours on the plot. Names should be identical to the categories or to the content of labelVec and the last one is per convention the reference.
`legendText`	positive numeric. Size of the legend text. Default: 0.92
`base_family`	character string. Name of the font to use. Default: "Linux Libertine"
`base_size`	positive numeric. Size of the font to use as a base.
`centerTitle`	boolean. Default:TRUE. Whether to centre the title or keep it on the left.
`out`	character string. Allows to chose the type of returned object. "plot" (default) for the plot and "annotatedPlot" for an annotated plot
`VinterO8`	boolean. Default: FALSE. Add a vertical line for 80 percent of the data