sortedGenesCorr: Plot the correlation of different studies comparison that are...
In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

sortedGenesCorr

R Documentation

Plot the correlation of different studies comparison that are ranked in decreasing order of correlation level.

Description

Plot the correlation of different studies comparison that are ranked in decreasing order of correlation level.

Usage

sortedGenesCorr(cor1, cor2, ref, simul1, simul2, seed = 1235,
  aggregateBool = FALSE, aggregMethod = "rowMeans", title = "",
  xtitle = "Rank (sorted by decreasing order of correlation)",
  ytitle = "", unit = " (PPKM)", base_family = "Linux Libertine",
  base_size = 11, legendText = 0.92, ColPalette, geneList,
  precomputed = FALSE, CorDF, out = "point")

Arguments

`cor1`	named numeric vector. Comprises all the correlations between two studies for each genes.
`cor2`	named numeric vector. Comprises all the correlations between two other studies for each genes.
`ref`	named numeric vector. Comprises all the correlations between two studies that can be used as reference.
`simul1`	named numeric vector or data.frame. Randomisation of cor1
`simul2`	named numeric vector or data.frame. Randomisation of cor2
`seed`	integer. Default: 1235. Allows to always pick the same simulation when data.frames are supplied.
`aggregateBool`	boolean. Default:FALSE. Whether all the simulations should be aggreagated in one value for each gene per data.frame
`aggregMethod`	character string for a funtion. Default:'rowMeans'.
`title`	character string. Title of the plot.
`xtitle`	character string. Label of the x-axis.
`ytitle`	character string. Label of the y-axis.
`unit`	character string. Unit in which the expression of the first study (Proteomics) is quantified
`base_family`	character string. Name of the font to use.
`base_size`	numeric. Size of the font to use (as a base)
`legendText`	numeric. Size of the legend text.
`ColPalette`	vector of character string to customise the colours of "cor1", "cor2","simul1",...
`geneList`	vector of character string. Gene identifiers that should be included in the figure. default: common ids between cor1, cor2, simul1, simul2 and ref
`precomputed`	boolean. Default:FALSE. Whether the data for the plot is already provided by CorDF
`CorDF`	data.frame already computed by a previous
`out`	character string. Either "point", "point_DF" or "density"