This function is used to create a ggplot2 bubble chart displaying the enrichment results.
enrichment_chart(
result_df,
top_terms = 10,
plot_by_cluster = FALSE,
num_bubbles = 4,
even_breaks = TRUE
)a data frame that must contain the following columns:
Description of the enriched term
Fold enrichment value for the enriched term
the lowest adjusted-p value of the given term over all iterations
the up-regulated genes in the input involved in the given term's gene set, comma-separated
the down-regulated genes in the input involved in the given term's gene set, comma-separated
the cluster to which the enriched term is assigned
number of top terms (according to the 'lowest_p' column)
to plot (default = 10). If plot_by_cluster = TRUE, selects the top
top_terms terms per each cluster. Set top_terms = NULL to plot
for all terms.If the total number of terms is less than top_terms,
all terms are plotted.
boolean value indicating whether or not to group the
enriched terms by cluster (works if result_df contains a
'Cluster' column).
number of sizes displayed in the legend # genes
(Default = 4)
whether or not to set even breaks for the number of sizes
displayed in the legend # genes. If TRUE (default), sets
equal breaks and the number of displayed bubbles may be different than the
number set by num_bubbles. If the exact number set by
num_bubbles is required, set this argument to FALSE
a ggplot2 object containing the bubble chart.
The x-axis corresponds to fold enrichment values while the y-axis indicates
the enriched terms. Size of the bubble indicates the number of significant
genes in the given enriched term. Color indicates the -log10(lowest-p) value.
The closer the color is to red, the more significant the enrichment is.
Optionally, if 'Cluster' is a column of result_df and
plot_by_cluster == TRUE, the enriched terms are grouped by clusters.
g <- enrichment_chart(example_pathfindR_output)
#> Plotting the enrichment bubble chart