Reference

Data

data_cell_cycle str()

RNA-seq data

Main Functions

These functions provide the results all other functions are built around, although many functions were designed to be used with self-produced data as well. The general order of operations is the same as the listed order.

precise_dist()

Create multiple distance matrices with optional resampling

precise_fusion()

Fuse multiple distance matrices into a single distance matrix

precise_graph()

Create a sparse, clustered graph from a distance matrix

precise_viz()

Visualize the results of precise_graph

General Helpers

These functions are not an explicit part of the PreciseDist workflow, but can be helpful for it’s successful completeion.

precise_dist_list()

Access the list of all built-in distances

precise_func_fact()

Create distance functions for input into precise_dist

precise_correlations()

Matrix correlations between multiple distance matrices

precise_transform()

Transformation functions for a list of distance matrices or the output of precise_dist

precise_cluster()

Create a sparse, clustered graph from a distance matrix

precise_stats()

Calculate data statistics

precise_features()

Calculate data statistics

TrelliscopeJS Helpers

These functions are set-up functions, so that we can utilize the small mutiples principle of data vizualization downstream to allow for efficent data interactions. While the results are meant to be used with precise_trellis they can also be useful as standalone functions.

precise_heatmap()

Run heatmap on the results of precise_dist

precise_tsne()

Run tsne on the results of precise_dist

precise_umap()

Run umap on the results of precise_dist

trellis_viz()

Create a trelliscopejs object populated by 2D plots

precise_descriptors()

Create a trelliscopejs object populated by descriptors

precise_distribs()

Create a trelliscopejs object populated by descriptors

precise_pivot()

Create a trellisopejs object populated by pivot tables.

TrelliscopeJS Wrapper

This function is a wrapper around TrelliscopeJS with a few additions. See https://hafen.github.io/trelliscopejs/index.html for more information about the output.

precise_trellis()

While trelliscopejs is a very powerful visualization paradigm, it can be hard to munge the data into the appropriate format. This function automatically creates a trelliscopejs visualization populated with pivot tables created by rpivotTable.

Miscellaneous

plotly_embed()

Images