diceR: graphs – R documentation

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graphs

Graphical Displays

Description

Graph cumulative distribution function (CDF) graphs, relative change in area under CDF curves, heatmaps, and cluster assignment tracking plots.

Usage

graph_cdf(mat)

graph_delta_area(mat)

graph_heatmap(mat, main = NULL)

graph_tracking(cl)

graph_all(x)

Arguments

`mat`	same as `x`, or a list of consensus matrices computed from `x` for faster results
`main`	heatmap title. If `NULL` (default), the titles will be taken from names in `mat`
`cl`	same as `x`, or a matrix of consensus classes computed from `x` for faster results
`x`	an object from `consensus_cluster()`

Details

graph_cdf plots the CDF for consensus matrices from different algorithms. graph_delta_area calculates the relative change in area under CDF curve between algorithms. graph_heatmap generates consensus matrix heatmaps for each algorithm in x. graph_tracking tracks how cluster assignments change between algorithms. graph_all is a wrapper that runs all graphing functions.

Value

Various plots from graph_*{} functions. All plots are generated using ggplot, except for graph_heatmap, which uses NMF::aheatmap(). Colours used in graph_heatmap and graph_tracking utilize RColorBrewer::brewer.pal() palettes.

Author(s)

Derek Chiu

References

https://stackoverflow.com/questions/4954507/calculate-the-area-under-a-curve

Examples

# Consensus clustering for 3 algorithms
library(ggplot2)
set.seed(911)
x <- matrix(rnorm(80), ncol = 10)
CC1 <- consensus_cluster(x, nk = 2:4, reps = 3,
algorithms = c("hc", "pam", "km"), progress = FALSE)

# Plot CDF
p <- graph_cdf(CC1)

# Change y label and add colours
p + labs(y = "Probability") + stat_ecdf(aes(colour = k)) +
scale_color_brewer(palette = "Set2")

# Delta Area
p <- graph_delta_area(CC1)

# Heatmaps with column side colours corresponding to clusters
CC2 <- consensus_cluster(x, nk = 3, reps = 3, algorithms = "hc", progress =
FALSE)
graph_heatmap(CC2)

# Track how cluster assignments change between algorithms
p <- graph_tracking(CC1)

diceR

Diverse Cluster Ensemble in R

v1.0.3

MIT + file LICENSE

Authors

Derek Chiu [aut, cre], Aline Talhouk [aut], Johnson Liu [ctb, com]

Initial release