plot_pair {dnapath} | R Documentation |
Plot the expression values of two genes
Description
Inspired by the plotCors
function from the DGCA package,
this function is used to plot the expression values of two genes contained
in the differential network analysis results. This is useful for comparing
the marginal relationship between two genes. Note, however, that this
visualization is not able to show conditional associations.
Usage
plot_pair(
x,
gene_A,
gene_B,
method = "loess",
alpha = 0.5,
se_alpha = 0.1,
use_facet = FALSE,
scales = "fixed"
)
Arguments
x |
A 'dnapath' or 'dnapath_list' object from |
gene_A |
The name of the first gene to plot. Must be one of the names
in |
gene_B |
The name of the second gene to plot. Must be one of the names
in |
method |
A charater string, either "lm" or "loess" (the default)
used by |
alpha |
Sets the transparancy of the points, used to set alpha in
|
se_alpha |
Sets the transparancy of the confidence band around the association trend line. Set to 0 to remove the band. |
use_facet |
If TRUE, the groups are plotted in separate graphs
using the |
scales |
Only used if do_facet_wrap is TRUE. See
|
Value
Plots the differential network and returns the ggplot object. Additional modifications can be applied to this object just like any other ggplot.
References
Grimes T, Datta S (2019). SeqNet: Generate RNA-Seq Data from Gene-Gene Association Networks. R package version 1.1.0, https://CRAN.R-project.org/package=SeqNet.
Examples
data(meso)
data(p53_pathways)
set.seed(0)
results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways,
group_labels = meso$groups, n_perm = 10)
# Plot of the marginal association between the first two genes.
genes <- get_genes(results)[1:2]
g <- plot_pair(results, genes[1], genes[2])
# The ggplot object, g, can be further modified.
# Here we move the legend and use a log scale for the expression values
# (the log scale doesn't help with these data but is shown for demonstration).
g <- g +
ggplot2::theme(legend.position = "bottom") +
ggplot2::scale_x_log10() +
ggplot2::scale_y_log10()
g