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

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()

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.

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.

References

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

Author

Derek Chiu

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)