Plot the summary metrics from get_metrics
plot_metrics.Rdplot_metrics creates plots of all the summary metrics calculated by get_metrics.
By making the 'metric_dfs_by_net' argument a list of multiple outputs from get_metrics,
you can plot the metrics from multiple networks on the same graphs.
The x-axis is based on the network subset sizes.
Usage
plot_metrics(
metric_dfs_by_net,
title_text,
subtitle_text = "",
perTF,
sum = TRUE,
percent = FALSE,
mean = FALSE,
median = FALSE,
annotation_overlap = FALSE,
size = TRUE
)Arguments
- metric_dfs_by_net
a list of outputs from
get_metrics- title_text
text for the title of every plot; generally the names of the networks
- subtitle_text
text for the subtitle of every plot
- perTF
boolean whether the network subset sizes were specified as average target genes per TF; changes the x-axis label
- sum
boolean whether to plot the 'sum' metric, which is the sum of the negative log base 10 of the p-value for the top term of each source node minus the penalty times the total number of source nodes.
- percent
boolean whether to plot the 'percent' metric, which is the percent of source nodes with at least one term with a FDR below a threshold
- mean
boolean whether to plot the 'mean' metric, which is the mean negative log base 10 of the p-value for the top term of each source node regardless of significance
- median
boolean whether to plot the 'median' metric, which is the median negative log base 10 of the p-value for the top term of each source node regardless of significance
- annotation_overlap
boolean whether to plot the 'annotation_overlap' metric, which is the percent of source nodes that are annotated to at least one of the 16 GO terms for which their target genes are most enriched
- size
boolean whether to plot the 'size' metric, which is the number of source nodes in the network subset that have more than one target gene with annotations