plot.term_enrichment_by_subset {RITAN} | R Documentation |
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)