gapmap: Functions for Drawing Gapped Cluster Heatmap with ggplot2

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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.

Author
Ryo Sakai
Date of publication
2016-12-05 18:28:47
Maintainer
Ryo Sakai <ryo@vda-lab.be>
License
GPL-2 | GPL-3
Version
0.0.4
URLs

View on CRAN

Man pages

as.gapdata
Make a gapdata class object
assign_branch_positions
Re-evaluate the position of branches
assign_positions
Re-evaluate the position of leaves
calculate_gap
Calculate the gaps based on distance
count_gap
Count the number of gaps based on a threshold
extract_list
Extract a list from the dendrogram object
format_number
Function to format a number
gap_data
Generate a gapdata class object from a dendrogram object
gap_dendrogram
Function to draw a gapped dendrogram
gap_heatmap
Function to draw a gapped heatmap
gap_label
Function to draw a gapped labels
gapmap
Function to draw a gapped cluster heatmap
gapmap-package
Draws gapped heatmap (gapmap) and gapped dendrograms using...
get_most_left_leaf
Get the most left leaf object from a dendrogram
get_most_right_leaf
Get the most right leaf object from a dendrogram
get_segment_df
Make a data.frame object
is.gapdata
Function to check if a object is a gapdata class object
map
A function to map values in a range
map.exp
A function to map values in a range exponentially
sample_tcga
Sample data matrix from the integrated pathway analysis of...
set_most_right_leaf
Set the most right leaf object from a dendrogram
sum_distance
Sum the distance of all branches in a dendrogram

Files in this package

gapmap
gapmap/inst
gapmap/inst/doc
gapmap/inst/doc/tcga_example.R
gapmap/inst/doc/simple_example.html
gapmap/inst/doc/tcga_example.Rmd
gapmap/inst/doc/tcga_example.html
gapmap/inst/doc/simple_example.R
gapmap/inst/doc/simple_example.Rmd
gapmap/NAMESPACE
gapmap/data
gapmap/data/sample_tcga.rda
gapmap/R
gapmap/R/gap_dendrogram.R
gapmap/R/is.gapdata.R
gapmap/R/assign_positions.R
gapmap/R/map.exp.R
gapmap/R/assign_branch_positions.R
gapmap/R/as.gapdata.R
gapmap/R/get_most_right_leaf.R
gapmap/R/map.R
gapmap/R/count_gap.R
gapmap/R/gap_heatmap.R
gapmap/R/get_most_left_leaf.R
gapmap/R/sum_distance.R
gapmap/R/extract_list.R
gapmap/R/gap_data.R
gapmap/R/gap_label.R
gapmap/R/gapmap-package.R
gapmap/R/calculate_gap.R
gapmap/R/gapmap.R
gapmap/R/format_number.R
gapmap/R/get_segment_df.R
gapmap/R/set_most_right_leaf.R
gapmap/vignettes
gapmap/vignettes/tcga_example.Rmd
gapmap/vignettes/simple_example.Rmd
gapmap/MD5
gapmap/build
gapmap/build/vignette.rds
gapmap/DESCRIPTION
gapmap/man
gapmap/man/assign_branch_positions.Rd
gapmap/man/extract_list.Rd
gapmap/man/set_most_right_leaf.Rd
gapmap/man/assign_positions.Rd
gapmap/man/map.Rd
gapmap/man/get_most_left_leaf.Rd
gapmap/man/gapmap-package.Rd
gapmap/man/format_number.Rd
gapmap/man/sample_tcga.Rd
gapmap/man/get_most_right_leaf.Rd
gapmap/man/is.gapdata.Rd
gapmap/man/get_segment_df.Rd
gapmap/man/gap_heatmap.Rd
gapmap/man/gap_dendrogram.Rd
gapmap/man/sum_distance.Rd
gapmap/man/gap_data.Rd
gapmap/man/as.gapdata.Rd
gapmap/man/gap_label.Rd
gapmap/man/calculate_gap.Rd
gapmap/man/count_gap.Rd
gapmap/man/map.exp.Rd
gapmap/man/gapmap.Rd