Usage
expression_plot( gene_id, result, eSet, x_var, f=result$factor, subset=NULL, xlab=x_var, ylab="log2(cpm)", ylim=range(exprs(eSet)), col.palette="Accent", col=brewer.pal(n=length(levels(pData(eSet)[,f])), name=col.palette), level=0.95, title=NULL, title.size=2, axis.title.size=20, axis.text.size=15, axis.text.angle=0, legend.title.size=20, legend.text.size=15, legend.key.size=30)
Arguments
gene_id
An gene or probeset identifier present in rownames(expr_data).
result
An output of the GO_analyse() or subset_scores() function.
eSet
ExpressionSet of the Biobase package including a
gene-by-sample expression matrix in the AssayData slot, and a
phenotypic information data-frame in the phenodate slot. In the
expression matrix, row names are Ensembl gene identifiers or probeset
identifiers, and column names are sample identifiers. In the phentypic
data-frame, row names are sample idenfifiers, column names are grouping
factors and phenotypic traits usable for the one-way ANOVA.
x_var
A column name in phenodata to plot on the X-axis. If representing
time on the X-axis, users should store the time-points as numeric values
in the AnnotatedDataFrame to adequately space the time-points.
f
A column name in phenodata to group the samples when representing
mean and confidence interval. The factor specified in the initial
GO_analyse() call is used by default. Unexpected grouping factors
of samples can reveal interesting trends (e.g. "Animal", "Tissue",
"CellType", ...).
subset
A named list to subset eSet. Names must be column names existing
in colnames(pData(eSet)). Values must be vectors of values existing in
the corresponding column of pData(eSet).
xlab
Title of the X-axis. Default is tha value of x_var.
ylab
Title of the Y-axis. Default is "log2(cpm)".
ylim
Numeric vector of length 2 specifying the lower and upper bounds of the
Y axis. Default is scaled to the full range of expression values in the
expression dataset, to ease comparison of different genes. If set to
NULL, the axis will be scaled to fit the plotted data only.
col.palette
A valid RColorBrewer palette name to fetch the colormap from.
Default is palette "Accent".
col
A vector of color names or codes. The number of colors provided must match
the number of levels of the grouping factor. If specified, overrides
argument col.palette.
level
The confidence interval level to visualise around the mean of each group.
Default is 0.95.
title
Changes the plot title. Default is a combination of the gene id and the
associated gene.
title.size
Changes the font size of the title. Default is 2.
axis.title.size
Changes the font size of the axes title. Defalt is 20.
axis.text.size
Changes the font size of the axes text labels. Default is 15.
axis.text.angle
Changes the angle of the X axis text labels. Default is 0 (horizontal).
legend.title.size
Changes the font size of the legend title. Default is 20.
legend.text.size
Changes the font size of the legend text labels. Default is 15.
legend.key.size
Changes the size of the legend keys (in points). Default is 30.