# Reconstruction of Clones from Integration Site Readouts and Visualization

## Documentation for package ‘MultIS’ version 0.6.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

bushmanplot | Create a stacked area plot that represents the abundance of integration sites over time.
bw | Calculate the bw index
convert_columnwise_relative | Converts a matrix to relative abundances
evaluate_clustering | Evaluate a clustering using the given method
evaluate_clustering_bw | Evaluate a clustering using the bw index
evaluate_clustering_custom | Evaluate a clustering using a custom evaluation function
evaluate_clustering_dunn | Evaluate a clustering using the dunn index
evaluate_clustering_ptbiserial | Evaluate a clustering using the point-biserial index
evaluate_clustering_sdindex | Evaluate a clustering using the SD-index
evaluate_clustering_silhouette | Evaluate a clustering using the silhouette index
filter_at_tp_biggest_n | Filters a matrix of readouts for the n biggest IS at a certain measurement
filter_at_tp_min | Filters a matrix of readouts for IS that have a minimum occurrence in some measurement
filter_combine_measurements | Combines columns that have the same name. The columns are joined additively.
filter_is_names | Shortens the rownames of a readout matrix to the shortest distinct prefix
filter_match | Filters for columns containing a certain substring.
filter_measurement_names | Splits a vector of strings by a given regexp, selects and rearranges the parts and joins them again
filter_names | Filters a vector of names and returns the shortest common prefix.
filter_nr_tp_min | Filters for a minimum number of time points/measurements
filter_zero_columns | Removes columns that only contain 0 or NA.
filter_zero_rows | Removes rows that only contain 0 or NA.
find_best_nr_cluster | Finds the best number of clusters according to silhouette
get_similarity_matrix | Generate a similarity matrix
ggplot_colors | Get the default ggplot color palette or a color palette based on the ggplot palette, but with sub-colors that differ in their luminance
lineplot_split_clone | Show line plots of all integration sites over time, split into facets by their respective clone.
normalize_timecourse | Normalizes a time course using a given mapping from integration sites to clones.
plot.clusterObj | Plots the clustering based on a clustering object
plot.ISSimilarity | Plots the similarity of integration sites
plot.timeseries | Plots time series data, which consists of multiple measurements over time / place (cols) of different clones / integration sites (rows).
plot_rsquare | Plots R^2 of two integration sites
reconstruct | Apply a clustering algorithm to a given time course.
reconstruct_kmedoid | Calculate the k-medoids clustering for a given time course.
reconstruct_recursive | Apply a clustering algorithm recursively to a given time course.
weighted_spring_model | Plot the relationship of integration sites as a graph.