plot_sct: Plot a sample-condition table

In steveneschrich/CLIApet: CLIA Performance Evaluation Toolkit: An R Library For Supporting Gene Expression Based CLIA Validation Studies

Description

Plot the gene expression data within a sample-condition table, indicating both the samples and conditions in the plot.

Usage

plot_sct(sct, sample_field = NULL, condition_field = NULL, main = NULL)

Arguments

sct	A sample-condition table.
sample_field	The string name of the sample field
condition_field	The string name of the condition field
main	a title for the plot

Details

sct stands for sample-condition table. Briefly, it collects information from an ExpressionSet into a set of samples with specific conditions, together with gene expression. This is really only useful for gene subset. Given the gene subset, you can then plot the genes by sample and by condition.

The samples are indicated by color and the conditions are indicates by shape. NOTE: if the condition is not specified, then just the samples are plotted (i.e., no conditions).

Also note that the samples and conditions have to be factors. This will be done by default for you. However, if you want a particular ordering of the levels then convert the column to a factor before calling the function.

NOTE: If you want a list, use plot_sct_by_sample()

Value

A ggplot showing the gene expression for a set of samples and conditions.

steveneschrich/CLIApet documentation built on March 2, 2021, 12:02 a.m.