plot.term_enrichment_by_subset: plot.term_enrichment_by_subset
In MTZimmer/RITAN: Rapid Integration of Term Annotation and Network resources

Description Usage Arguments Value Examples

plot.term_enrichment_by_subset

## S3 method for class 'term_enrichment_by_subset'
plot(x, show_values = TRUE,
  annotation_matrix = NA, low = "white", high = "#2166AC",
  return_ggplot_object = FALSE, label_size_x = 16, label_angle_x = -30,
  label_size_y = 9, wrap_y_labels = 20, grid_line_color = "white",
  mid = 0, cap = NA, annotation_palates = c("Reds", "Greens", "Purples",
  "Greys", "BuPu", "RdPu", "BrBG", "PiYG", "Spectral"),
  annotation_legend_x = -0.3, ...)

`x`	data frame returned by term_enrichment_by_subset
`show_values`	True or False, plot values on the heatmap
`annotation_matrix`	a matrix() of group-levle characteristics - same number of columns as "m"
`low`	color for low end of range
`high`	color for high end of range
`return_ggplot_object`	logical flag (default FALSE) that if TRUE, the ggplot object for the plot is returned
`label_size_x`	size of text for x label. Default lable_size_x=16
`label_angle_x`	angle for text for x label. Default is -30 degrees
`label_size_y`	size of text for y label. Default label_size_y=9
`wrap_y_labels`	Number of characters to wrap row labels
`grid_line_color`	color o grid lines between cells. Default is white.
`mid`	sets lower threshold for color scale
`cap`	Clip numeric values to this maximum threshold
`annotation_palates`	Color palates (RColorBrewer) used for each row of the annotation matrix
`annotation_legend_x`	offset for placing the legend
`...`	further areguments are not used at this time. If the user wants to modify the plot, use return_ggplot_object = TRUE.

silent return, unless return_ggplot_object==TRUE. Then, the ggplot object for the plot is returned.

## Create list of gene sets to evaluate.
##   This example is from a vaccine study where we pre-generated differentially expressed genes.
##   This object will be passed to the groups parameter.
require(RITANdata)
vac1.de.genes <- list(vac1.day0vs31.de.genes, vac1.day0vs56.de.genes)
names(vac1.de.genes) <- c("Day0vs31", "Day0vs56")
print(str(vac1.de.genes))

## Not run: 
## Run term_enrichment_by_subset on the two results.
##   This function usually takes a few seconds to a minute to run.
m <- term_enrichment_by_subset(groups = vac1.de.genes, q_value_threshold = .9)
summary(m)
plot( m, label_size_y = 4, show_values = FALSE )

## End(Not run)