expression_plot_symbol: Plots the expression profile of a gene by levels of a factor

Description Usage Arguments Value Warning Author(s) References See Also Examples

View source: R/post_analysis.R

Description

This function will plot the expression profile of a gene across a valid X-axis variable from the AnnotatedDataFrame while representing the mean and confidence interval of groups of samples defined by levels of a valid grouping factor from the AnnotatedDataFrame.

In the case of a gene name represented by multiple gene or probeset identifiers in the dataset, a lattice of plots will be produced. Each of the plots in this lattice can subsequently be plotted separately using its associated index.

Usage

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expression_plot_symbol(
    gene_symbol, result, eSet, x_var, f=result$factor, subset=NULL,
    index=0, 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, titles=c(), title.size=2, axis.title.size=20,
    axis.text.size=15, axis.text.angle=0,
    legend.title.size=20, legend.text.size=20, legend.key.size=30)

Arguments

gene_symbol

A gene name present in rownames(AlvMac_results$genes).

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).

index

In the case where multiple gene or probeset identifiers are associated with the gene name, index=2 will plot the expression profile of the second feature identifier alone, for instance.

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.

col

A vector of color names or codes. The number of colors provided must match the number of levels of the grouping factor. Default to a palette with an adequate set of colors. If specified, overrides argument col.palette.

level

The confidence interval level to visualise around the mean of each group. Default is 0.95.

titles

Character vector providing as many titles as there are plots to replace the default titles. 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.

Value

The ggplot object, or the vector of feature identifiers if multiple features are annotated to the gene symbol.

Warning

Common issues:

Author(s)

Kevin Rue-Albrecht

References

See Also

Packages Biobase and ggplot2 , methods expression_plot and GO_analyse.

Examples

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# load the sample output data
data(AlvMac_results)

# Expression by gene identifier (TNIP3)
expression_plot_symbol(
    gene_symbol="PIK3AP1",
    result=AlvMac_results, eSet=AlvMac, x_var="Timepoint"
    )

# Same gene, plotted by animal and grouped by treatment (merging time points)
expression_plot_symbol(
    gene_symbol="PIK3AP1",
    result=AlvMac_results, eSet=AlvMac, x_var="Animal",
    f="Treatment"
    )

# Same gene, plotted by animal and grouped by time-point (merging treatments)
expression_plot_symbol(
    gene_symbol="PIK3AP1",
    result=AlvMac_results, eSet=AlvMac, x_var="Animal",
    f="Time")

kevinrue/GOexpress-release documentation built on May 20, 2019, 9:08 a.m.