View source: R/AntibodyForests_plot_metrics.R
AntibodyForests_plot_metrics | R Documentation |
Will plot the resulting node metrics from the AntibodyForests_metrics function either as violin plots (plot.format = 'violin' or as a scatter plot of the principal components of the metrics dataframe - as long as multiple node metrics are calculated per node). Requires the AntibodyForests_plot_metrics to be called before (as this function uses the resulting node_metrics dataframes).
AntibodyForests_plot_metrics( trees, plot.format, metrics.to.plot, group.by, max.groups, specific.groups, sample.by, features )
trees |
nested list of AntibodyForests objects or single object, as obtained from the AntibodyForests function. |
plot.format |
string - 'violin' for violin plots of node metrics per feature (as determined by the feature parameter), or 'pca' for performing PCA on the node metrics dataframe. |
metrics.to.plot |
vector of strings - the metrics to be plotted from the metrics dataframe (must be already calculated using the AntibodyForests_metrics function) |
group.by |
string - whether to group the violin/scatter plots by additional features (e.g., group.by = 'sample_id' to get violin plots per feature, per each unique sample). |
max.groups |
integer - maximum number of groups to be considered in the resulting plots if group.by is not NULL. |
specific.groups |
vector of strings - specific groups to plot if group.by is not NULL. |
sample.by |
string - additional grouping factor (e.g., group.by can be set to 'clonotype_id' and sample.by to 'sample_id' for plots grouped by both clonotypes and samples) |
features |
string - will determine the point colors in the PCA scatterplot. |
either a violin plot or a scatter plot of the node metrics, as specified in the plot.format parameter
## Not run: AntibodyForests_plot_metrics(trees, plot.format = 'violin', metrics.to.plot = 'degree', group.by = 'sample_id', sample.by = NULL) ## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.