cumulSpeSimulAggregated: Plot the course of TS proteins when the level of genes...
In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

cumulSpeSimulAggregated

R Documentation

Plot the course of TS proteins when the level of genes correlation varies

Description

Plot the course of TS proteins when the level of genes correlation varies

Usage

cumulSpeSimulAggregated(cor1, breadthExp, simul1, reference, cor2, simul2,
  aggregMethod = "rowMeans", Title, CorrelationPlot = TRUE,
  relabel = TRUE, labelVec = setNames(c("Protein/mRNA pairs",
  "mRNA/mRNA pairs ('ideal' reference)", "Randomised Protein/mRNA pairs"),
  c("Cor", "reference", "Simul")), sizeLine = 1.1, palette,
  legendText = 0.92, base_family = "Linux Libertine", base_size = 11,
  centerTitle = TRUE, out = "plot")

Arguments

`cor1`	named numeric vector that comprises the correlation between two studies.
`breadthExp`	named postive integer that comprises the breadth of expression of the proteins
`simul1`	named numeric vector that comprises the result of the random permutations on cor1
`reference`	named numeric vector that comprises the correlation between two (transcriptomic) studies that can be used as a reference
`cor2`	named numeric vector that comprises the correlation between two studies.
`simul2`	named numeric vector that comprises the result of the random permutations on cor2
`aggregMethod`	character string for the name of the method to aggregate the different simulation together. Default: 'rowMeans'
`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
`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.
`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, "shortDF" for the data.frame, "DF" for the data.frame with all the initial data for the plot, and "annotatedPlot" for an annotated plot