nbGenesPerCond.unique: Plot the distribution of genes across the columns. Genes...

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

Plot the distribution of genes across the columns. Genes found uniquely in one condition are highlighted in another colour.

Description

Plot the distribution of genes across the columns. Genes found uniquely in one condition are highlighted in another colour.

Usage

nbGenesPerCond.unique(DF, reorder = TRUE, xlab = "Tissue", ylab, title,
  legend.title = "Gene is", publish = TRUE, threshold = 0, thm, Y,
  remove.legend = FALSE, legendPosition = "bottom", out = "DF",
  print = TRUE)

Arguments

DF	numerical data.frame. Rownames have to be meaningful.
reorder	boolean; default: TRUE. Whether the columns should be reorder by the number of expressed genes instead of their names.
xlab	character string; used as x-axis label.
ylab	character string; used as y-axis label.
title	character string; title of the plot.
legend.title	character string; what to use for the colour legend
publish	boolean; default: TRUE. Applies theme_bw to the plot.
threshold	numeric; default: 0. Minimal level of expression to be considered as an expressed gene
thm	other theme object (theme) to pass on to the plot
Y	numeric vector of two elements. Specify the limites of the y-axis. 'c(minimal limit value, maximal limit value)'
remove.legend	boolean; default: TRUE. Whether the legend should be removed (do not impact the plot)
legendPosition	either 'top','right','bottom' or 'left'. Where to position the legend.
out	switch to chose the type of object returned by the function; default 'DF', i.e. the data.frame with the formatted data used for the plotting. Other options are: 'legend' for the legend of the plot, 'plot' for the figure itself, 'plot_noLegend' for the plot without the legend, 'plot_data' for the ggtable data to recreate the plot
print	boolean; default: TRUE. Whether the plot should be printed

Value

depends on 'out' : 'DF' returns the data.frame with all the required information for the plot, 'legend' the legend of the plot, 'plot' the figure itself, 'plot_noLegend', the plot without the legend, 'plot_data' the ggtable data to recreate the plot

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