complement2nbGenesPerCond.unique: Facetted plot (e.g. per study) of the distribution of genes...

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

Facetted plot (e.g. per study) of the distribution of genes across the columns. Genes found uniquely in one condition are highlighted in another colour.

Description

Facetted plot (e.g. per study) of the distribution of genes across the columns. Genes found uniquely in one condition are highlighted in another colour.

Usage

complement2nbGenesPerCond.unique(DF, xlab, ylab, title, legend.title,
  publish = TRUE, threshold = 0, thm, Y, remove.legend = FALSE,
  out = "DF", print = TRUE, facetting = "Study", flip = FALSE)

Arguments

DF	numerical data.frame. Rownames have to be meaningful. Collates many columns from several studies.
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; used for the colour legend title
publish	boolean. Default: TRUE.
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: FALSE.
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 'plot_def' for the output of ggplot_build on the plot
print	boolean; default: TRUE. Whether the plot should be printed
facetting	character string; name of the column that should be used for the facetting.
flip	boolean. Default= FALSE. Whether the x-axis and y-axis should be flipped or not.

Value

depends on out. Objects/plot similar to nbGenesPerCond.unique with facetting for the different studies in the original dataframe.

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