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gapmap (version 0.0.4)

Functions for Drawing Gapped Cluster Heatmap with ggplot2

Description

The gap encodes the distance between clusters and improves interpretation of cluster heatmaps. The gaps can be of the same distance based on a height threshold to cut the dendrogram. Another option is to vary the size of gaps based on the distance between clusters.

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Version

Install

install.packages('gapmap')

Monthly Downloads

1,102

Version

0.0.4

License

GPL-2 | GPL-3

Maintainer

Ryo Sakai

Last Published

December 5th, 2016

Functions in gapmap (0.0.4)

gap_data

Generate a gapdata class object from a dendrogram object
map.exp

A function to map values in a range exponentially
get_most_right_leaf

Get the most right leaf object from a dendrogram
assign_positions

Re-evaluate the position of leaves
format_number

Function to format a number
assign_branch_positions

Re-evaluate the position of branches
extract_list

Extract a list from the dendrogram object
gapmap-package

Draws gapped heatmap (gapmap) and gapped dendrograms using ggplot2 in [R].
sum_distance

Sum the distance of all branches in a dendrogram
as.gapdata

Make a gapdata class object
get_segment_df

Make a data.frame object
gapmap

Function to draw a gapped cluster heatmap
is.gapdata

Function to check if a object is a gapdata class object
gap_dendrogram

Function to draw a gapped dendrogram
get_most_left_leaf

Get the most left leaf object from a dendrogram
calculate_gap

Calculate the gaps based on distance
sample_tcga

Sample data matrix from the integrated pathway analysis of gastric cancer from the Cancer Genome Atlas (TCGA) study.
count_gap

Count the number of gaps based on a threshold
gap_label

Function to draw a gapped labels
set_most_right_leaf

Set the most right leaf object from a dendrogram
gap_heatmap

Function to draw a gapped heatmap
map

A function to map values in a range