plot_gene_pair: Scatter plot of two gene expressions
In tgrimes/SeqNet: Generate RNA-Seq Data from Gene-Gene Association Networks

Description Usage Arguments Value Examples

Plots the expression of two genes for visual assessment of association.

1 2	plot_gene_pair(x_list, geneA, geneB, method = "loess", se_alpha = 0.1, do_facet_wrap = FALSE, scales = "fixed")

`x_list`	A named list containing one or more n by p gene expression profiles, one for each group or subpopulation under consideration.
`geneA`	The name of the first gene to plot. Must be either a character string matching a column name in each matrix of x_list or an integer to index the columns.
`geneB`	The name of the second gene to plot. Must be either a character string matching a column name in each matrix of x_list or an integer to index the columns.
`method`	Charater string either "lm" or "loess" used for plotting. For no line, set method = NULL.
`se_alpha`	Sets transparancy of confidence interval around association trend line. Set to 0 to remove the confidence interval.
`do_facet_wrap`	If TRUE, the groups are plotted in seperate graphs.
`scales`	Only used if do_facet_wrap is TRUE. See ggplot2::facet_wrap for details.

Returns the generated plot.

data(reference)
rnaseq <- reference$rnaseq
genes <- colnames(rnaseq)
plot_gene_pair(rnaseq, genes[1], genes[2])
# Suppose we had multiple data frames.
control <- rnaseq[1:100, 1:10]
treatment1 <- rnaseq[101:200, 1:10]
treatment2 <- rnaseq[201:250, 1:10]
plot_gene_pair(list(ctrl = control, trt1 = treatment1, trt2 = treatment2),
               genes[1], genes[2], method = NA)
plot_gene_pair(list(ctrl = control, trt = treatment1),
               genes[1], genes[2], do_facet_wrap = TRUE, method = "lm")