evolCvCorrCumul: Plot the correlation of the gene expression while taking in...
In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

evolCvCorrCumul

R Documentation

Plot the correlation of the gene expression while taking in account the coefficient of variation of the genes between the same tissues of two studies as a function of the number of genes included in the correlation computation which varies based on the minimal threshold of expression of the genes.

Description

Plot the correlation of the gene expression while taking in account the coefficient of variation of the genes between the same tissues of two studies as a function of the number of genes included in the correlation computation which varies based on the minimal threshold of expression of the genes.

Usage

evolCvCorrCumul(DFa, cvDF, sepSeq, step = 0.01, method = "pearson",
  use = "pairwise.complete.obs", filename,
  fontfamily = "Linux Libertine", Colorpalette, legend = FALSE,
  point = FALSE, line = FALSE, smooth = TRUE)

Arguments

`DFa`	data.frame that contains the expression data for one tissue across several studies
`cvDF`	data.frame that contains the coefficient of variation of the different genes across the tissues
`sepSeq`	positive integer vector. Give the indices of the genes for which the expression should be plotted once ordered.
`step`	positive integer. The step to use between the rank to plot.
`method`	a character string indicating which correlation coefficient is to be computed. One of "pearson", "kendall" or "spearman".
`use`	character string which allows to pick the way missing data are handled. one of the strings "everything", "all.obs", "complete.obs", "na.or.complete", or "pairwise.complete.obs".
`filename`	character string. Path where the figure should be saved.
`fontfamily`	character string, name of the font to use. Default: "Linux Libertine"
`Colorpalette`	Named vector of character strings that allows to customise the colours in the plot
`legend`	boolean. Default: FALSE. Whether the legend should be added to the plot.
`point`	boolean. Default: FALSE. Whether to plot with geom_point()
`line`	boolean. Default: FALSE. Whether to plot with geom_line()
`smooth`	boolean. Default: TRUE. Whether to use a smooth line.