evolCorrCumul: Plot the correlation of the gene expression between the same...

In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

Plot the correlation of the gene expression 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 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

evolCorrCumul(DFa, sepSeq, step = 10, method = "pearson",
  use = "pairwise.complete.obs", filename,
  fontfamily = "Linux Libertine", fontSize = 11, simple = FALSE,
  sep = "(", verbose = FALSE, position.legend = "bottom",
  legendN = 2, point = TRUE, smooth = FALSE, line = FALSE,
  noTitleLegend = TRUE, Colorpalette, logscaleX = FALSE, ylabTitle,
  shorten = FALSE, Title, unit)

Arguments

DFa	data.frame that contains the expression data for one tissue across several studies
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"
fontSize	positive numeric. Size of the font to use as a base.
simple	boolean. Default: FALSE. Whether to simplify the plot.
sep	character string. Default: '('. Allows to retrieve the name of the study from the colnames (preformated colnames)
verbose	boolean. Default: FALSE. output additional messages.
position.legend	character string. Where to position the legend in regard of the plot. Default: "bottom", can be also 'right', 'left' and 'top'.
legendN	positive integer. Allows to apply a number of rows to the legend.
point	boolean. Default: TRUE. Whether to draw the curves as a separate point for each value
smooth	boolean. Default:FALSE. Whether to add a smooth line ("lm" method)
line	boolean. Default:FALSE. Whether to draw the curves as lines.
noTitleLegend	boolean. Default: TRUE. Whether to remove the title legend.
Colorpalette	Named vector of character strings that allows to customise the colours in the plot
logscaleX	boolean. Default: FALSE. Whether to apply a log10 transformation to the x-axis scale.
ylabTitle	character string. Allows to redefine the label of the y-axis.
shorten	boolean. Default: FALSE. Allows to shorten the names of the plotted objects (columns)
Title	character string. Title of the plot
unit	character string. Allows to fill in the unit in which the genes are quantified

Value

a figure

barzine/barzinePhdR documentation built on Nov. 23, 2024, 8:54 p.m.