## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", out.width = "100%", fig.asp = 0.4, fig.width = 8.766 ) ## ----setup, message=FALSE, warning=FALSE-------------------------------------- library(clugenr) # The clugenr library options(rgl.useNULL = TRUE) # Create RGL plots in systems without displays (CI) library(rgl) setupKnitr(autoprint = TRUE) # Render RGL plots directly on generated page # Load helper functions for plotting examples source("plot_examples_3d.R", local = knitr::knit_global()) # Keep examples reproducible in newer R versions RNGversion("3.6.0") ## ----------------------------------------------------------------------------- seed <- 123 ## ----------------------------------------------------------------------------- e043 <- clugen(3, 4, 300, c(1, 0, 0), 0, c(10, 10, 10), 15, 1.5, 0.5, seed = seed) e044 <- clugen(3, 4, 300, c(1, 1, 1), 0, c(10, 10, 10), 15, 1.5, 0.5, seed = seed) e045 <- clugen(3, 4, 300, c(0, 0, 1), 0, c(10, 10, 10), 15, 1.5, 0.5, seed = seed) ## ----------------------------------------------------------------------------- plot_examples_3d(list(e = e043, t = "e043: direction = [1, 0, 0]"), list(e = e044, t = "e044: direction = [1, 1, 1]"), list(e = e045, t = "e045: direction = [0, 0, 1]")) ## ----------------------------------------------------------------------------- seed <- 123 ## ----------------------------------------------------------------------------- # Custom angle_deltas function: arbitrarily rotate some clusters by 90 degrees angdel_90 <- function(nclu, astd) sample(c(0, pi / 2), nclu, replace = TRUE) ## ----------------------------------------------------------------------------- e046 <- clugen(3, 6, 300, c(1, 0, 0), 0, c(10, 10, 10), 15, 1.5, 0.5, seed = seed) e047 <- clugen(3, 6, 300, c(1, 0, 0), pi / 8, c(10, 10, 10), 15, 1.5, 0.5, seed = seed) e048 <- clugen(3, 6, 300, c(1, 0, 0), 0, c(10, 10, 10), 15, 1.5, 0.5, seed = seed, angle_deltas_fn = angdel_90) ## ----------------------------------------------------------------------------- plot_examples_3d(list(e = e046, t = "e046: angle_disp = 0"), list(e = e047, t = "e047: angle_disp = π / 8"), list(e = e048, t = "e048: custom angle_deltas function")) ## ----------------------------------------------------------------------------- seed <- 123 ## ----------------------------------------------------------------------------- # Define a main direction for each cluster dirs <- matrix(c(1, 1, 1, 0, 0, 1, 1, 0, 0, 0, 1, 0, -1, 1, 1), nrow = 5, byrow = TRUE) ## ----------------------------------------------------------------------------- e049 <- clugen(3, 5, 400, dirs, 0, rep.int(0, 3), 20, 0, 0.25, seed = seed) e050 <- clugen(3, 5, 400, dirs, pi / 12, rep.int(0, 3), 20, 0, 0.25, seed = seed) e051 <- clugen(3, 5, 400, dirs, pi / 4, rep.int(0, 3), 20, 0, 0.25, seed = seed) ## ----------------------------------------------------------------------------- plot_examples_3d(list(e = e049, t = "e049: angle_disp = 0"), list(e = e050, t = "e050: angle_disp = π / 12"), list(e = e051, t = "e051: angle_disp = π / 4")) ## ----------------------------------------------------------------------------- seed <- 123 ## ----------------------------------------------------------------------------- e052 <- clugen(3, 5, 300, c(1, 0, 0), pi / 10, c(10, 10, 10), 0, 0, 0.5, seed = seed, point_dist_fn = "n") e053 <- clugen(3, 5, 300, c(1, 0, 0), pi / 10, c(10, 10, 10), 10, 0, 0.5, seed = seed, point_dist_fn = "n") e054 <- clugen(3, 5, 300, c(1, 0, 0), pi / 10, c(10, 10, 10), 30, 0, 0.5, seed = seed, point_dist_fn = "n") ## ----------------------------------------------------------------------------- plot_examples_3d(list(e = e052, t = "e052: llength = 0"), list(e = e053, t = "e053: llength = 10"), list(e = e054, t = "e054: llength = 30")) ## ----------------------------------------------------------------------------- # Custom llengths function: line lengths tend to grow for each new cluster llen_grow <- function(nclu, llen, llenstd) { llen * (0:(nclu - 1) + rnorm(nclu, sd = llenstd)) } ## ----------------------------------------------------------------------------- e055 <- clugen(3, 5, 300, c(1, 0, 0), pi / 10, c(10, 10, 10), 15, 0.0, 0.5, seed = seed, point_dist_fn = "n") e056 <- clugen(3, 5, 300, c(1, 0, 0), pi / 10, c(10, 10, 10), 15, 10.0, 0.5, seed = seed, point_dist_fn = "n") e057 <- clugen(3, 5, 300, c(1, 0, 0), pi / 10, c(10, 10, 10), 10, 0.1, 0.5, seed = seed, point_dist_fn = "n", llengths_fn = llen_grow) ## ----------------------------------------------------------------------------- plot_examples_3d(list(e = e055, t = "e055: llength_disp = 0.0"), list(e = e056, t = "e056: llength_disp = 10.0"), list(e = e057, t = "e057: custom llengths function")) ## ----------------------------------------------------------------------------- seed <- 321 ## ----------------------------------------------------------------------------- e058 <- clugen(3, 8, 300, c(1, 1, 1), pi / 4, c(30, 10, 10), 25, 4, 3, seed = seed) e059 <- clugen(3, 8, 300, c(1, 1, 1), pi / 4, c(10, 30, 10), 25, 4, 3, seed = seed) e060 <- clugen(3, 8, 300, c(1, 1, 1), pi / 4, c(10, 10, 30), 25, 4, 3, seed = seed) ## ----------------------------------------------------------------------------- plot_examples_3d(list(e = e058, t = "e058: cluster_sep = [30, 10, 10]"), list(e = e059, t = "e059: cluster_sep = [10, 30, 10]"), list(e = e060, t = "e060: cluster_sep = [10, 10, 30]")) ## ----------------------------------------------------------------------------- seed <- 321 ## ----------------------------------------------------------------------------- # Custom clucenters function: places clusters in a diagonal centers_diag <- function(nclu, csep, coff) { matrix(1, nrow = nclu, ncol = length(csep)) * (1:nclu * max(csep)) + rep(coff, each = nclu) } ## ----------------------------------------------------------------------------- e061 <- clugen(3, 8, 300, c(1, 1, 1), pi / 4, c(10, 10, 10), 12, 3, 2.5, seed = seed) e062 <- clugen(3, 8, 300, c(1, 1, 1), pi / 4, c(10, 10, 10), 12, 3, 2.5, seed = seed, cluster_offset = c(20, -20, 20)) e063 <- clugen(3, 8, 300, c(1, 1, 1), pi / 4, c(10, 10, 10), 12, 3, 2.5, seed = seed, cluster_offset = c(-50, -50, -50), clucenters_fn = centers_diag) ## ----------------------------------------------------------------------------- plot_examples_3d(list(e = e061, t = "e061: default"), list(e = e062, t = "e062: cluster_offset = [20, -20, 20]"), list(e = e063, t = "e063: custom clucenters function"))