🎨 Remove library() from demo

demo/early.R

@@ -1,6 +1,3 @@
-library(tidyverse)
-library(tumopp)
-
 .args = list(
   "-D2 -k100 -Cmoore -Lconst -R256 -N256 -o Cmoore_Lconst",
   "-D2 -k100 -Cmoore -Lstep -R256 -N256 -o Cmoore_Lstep",
@@ -9,8 +6,8 @@ library(tumopp)
   "-D2 -k100 -Chex -Lstep -R256 -N256 -o Chex_Lstep",
   "-D2 -k100 -Chex -Llinear -R256 -N256 -o Chex_Llinear"
 )
-results = tumopp(.args)
-write_results(results)
+results = tumopp::tumopp(.args)
+# tumopp::write_results(results)
 
 .add_clade_to_snapshots = function(population, graph, snapshots, ...) {
   clade_info = tumopp:::sort_clades(population, graph, 4L)
@@ -20,13 +17,13 @@ write_results(results)
 
 .plot_snapshot = function(data, limit) {
   tumopp::plot_lattice2d(data, "clade", alpha = 1.0, limit = limit) +
-    scale_colour_brewer(palette = "Spectral", na.value = "grey50", guide = FALSE) +
-    theme_void()
+    ggplot2::scale_colour_brewer(palette = "Spectral", na.value = "grey50", guide = FALSE) +
+    ggplot2::theme_void()
 }
 
 .plot_snapshots = function(.tbl) {
   .lim = tumopp::max_abs_xyz(.tbl)
-  tidyr::nest(.tbl, !"time")$data |>
+  tidyr::nest(.tbl, data = !"time")$data |>
     parallel::mclapply(.plot_snapshot, limit = .lim)
 }
 
@@ -47,7 +44,7 @@ magick_gif_animation = function(infiles, outfile = "animation.gif", delay = 15,
   purrr::iwalk(.plt, \(.x, .y) {
     .outfile = file.path(.pngdir, sprintf("snapshot_%03d.png", .y))
     message(.outfile)
-    ggsave(.outfile, .x, width = 1, height = 1, scale = 6, dpi = 72)
+    ggplot2::ggsave(.outfile, .x, width = 1, height = 1, scale = 6, dpi = 72)
   })
   .infiles = file.path(.pngdir, "snapshot_*.png")
   magick_gif_animation(.infiles, sprintf("%s/%s.gif", outdir, outdir), delay = 8)

demo/rgl.R

@@ -1,71 +1,67 @@
 # !/usr/bin/env Rscript
-library(tidyverse)
-library(rgl)
-library(tumopp)
 
-######## 1#########2#########3#########4#########5#########6#########7#########
 ## transformation
 
 rgl::close3d()
 rgl::open3d(windowRect = c(0, 0, 600, 600))
 rgl::clear3d()
 rgl::view3d(70, 5, 60)
-axes3d()
+rgl::axes3d()
 .r = 2
-tibble(x = seq(-.r, .r), y = x, z = x) |>
+tibble::tibble(x = seq(-.r, .r), y = x, z = x) |>
   tidyr::expand(x, y, z) |>
   tumopp:::trans_coord_hcc() |>
   # tumopp:::trans_coord_fcc() |>
   dplyr::mutate(r = sqrt(x * x + y * y + z * z)) |>
-  with(spheres3d(x, y, z, color = "#009999", radius = 0.51, alpha = 0.6))
-title3d("", "", "x", "y", "z")
+  with(rgl::spheres3d(x, y, z, color = "#009999", radius = 0.51, alpha = 0.6))
+rgl::title3d("", "", "x", "y", "z")
 
 ######## 1#########2#########3#########4#########5#########6#########7#########
 ## minimum
 
-.hex_xy = read_csv("x,y,z\n0,0,0\n1,0,0\n0,1,0\n1,0,-1")
+.hex_xy = readr::read_csv(I("x,y,z\n0,0,0\n1,0,0\n0,1,0\n1,0,-1"))
 
 rgl::close3d()
 rgl::open3d(windowRect = c(0, 0, 600, 600))
 rgl::clear3d()
 rgl::view3d(20, 10, 60)
-axes3d()
+rgl::axes3d()
 .hex_xy |>
-  trans_coord_hex() |>
-  with(spheres3d(x, y, z, color = "#009999", radius = 0.51, alpha = 0.6))
-title3d("", "", "x", "y", "z")
+  tumopp::trans_coord_hex() |>
+  with(rgl::spheres3d(x, y, z, color = "#009999", radius = 0.51, alpha = 0.6))
+rgl::title3d("", "", "x", "y", "z")
 
 ######## 1#########2#########3#########4#########5#########6#########7#########
 ## neighbors
 
-.hex_xy = read_csv("x,y,z\n0,0,0\n0,1,0\n0,-1,0\n-1,0,0\n-1,1,0\n1,0,0\n1,-1,0")
+.hex_xy = readr::read_csv(I("x,y,z\n0,0,0\n0,1,0\n0,-1,0\n-1,0,0\n-1,1,0\n1,0,0\n1,-1,0"))
 
 rgl::close3d()
 rgl::open3d(windowRect = c(0, 0, 600, 600))
 rgl::clear3d()
 rgl::view3d(20, 10, 60)
-axes3d()
+rgl::axes3d()
 .hex_xy |>
-  bind_rows(.hex_xy |> dplyr::filter(x > 0 | (x == 0 & y == 0)) |> mutate(z = -1)) |>
-  bind_rows(.hex_xy |> dplyr::filter(x < 0 | (x == 0 & y == 0)) |> mutate(z = 1)) |>
+  dplyr::bind_rows(.hex_xy |> dplyr::filter(x > 0 | (x == 0 & y == 0)) |> dplyr::mutate(z = -1)) |>
+  dplyr::bind_rows(.hex_xy |> dplyr::filter(x < 0 | (x == 0 & y == 0)) |> dplyr::mutate(z = 1)) |>
   print() |>
   tumopp:::trans_coord_fcc() |>
-  with(spheres3d(x, y, z, color = "#009999", radius = 0.51, alpha = 0.6))
-title3d("", "", "x", "y", "z")
+  with(rgl::spheres3d(x, y, z, color = "#009999", radius = 0.51, alpha = 0.6))
+rgl::title3d("", "", "x", "y", "z")
 
 
 rgl::close3d()
 rgl::open3d(windowRect = c(0, 0, 600, 600))
 rgl::clear3d()
 rgl::view3d(40, 20, 60)
-axes3d()
+rgl::axes3d()
 .hex_xy |>
-  bind_rows(.hex_xy |> mutate(z = -1) |> dplyr::filter(x < 0 | (x == 0 & y == 0))) |>
-  bind_rows(.hex_xy |> mutate(z = 1) |> dplyr::filter(x < 0 | (x == 0 & y == 0))) |>
+  dplyr::bind_rows(.hex_xy |> dplyr::mutate(z = -1) |> dplyr::filter(x < 0 | (x == 0 & y == 0))) |>
+  dplyr::bind_rows(.hex_xy |> dplyr::mutate(z = 1) |> dplyr::filter(x < 0 | (x == 0 & y == 0))) |>
   print() |>
-  bind_rows(.hex_xy |> mutate(z = 5)) |>
-  bind_rows(.hex_xy |> mutate(z = 4) |> dplyr::filter(x > 0 | (x == 0 & y == 0))) |>
-  bind_rows(.hex_xy |> mutate(z = 6) |> dplyr::filter(x > 0 | (x == 0 & y == 0))) |>
+  dplyr::bind_rows(.hex_xy |> dplyr::mutate(z = 5)) |>
+  dplyr::bind_rows(.hex_xy |> dplyr::mutate(z = 4) |> dplyr::filter(x > 0 | (x == 0 & y == 0))) |>
+  dplyr::bind_rows(.hex_xy |> dplyr::mutate(z = 6) |> dplyr::filter(x > 0 | (x == 0 & y == 0))) |>
   tumopp:::trans_coord_hcc() |>
-  with(spheres3d(x, y, z, color = "#009999", radius = 0.51, alpha = 0.6))
-title3d("", "", "x", "y", "z")
+  with(rgl::spheres3d(x, y, z, color = "#009999", radius = 0.51, alpha = 0.6))
+rgl::title3d("", "", "x", "y", "z")

demo/run.R

@@ -1,35 +1,30 @@
-library(tidyverse)
-library(tumopp)
-
-tumopp("-h")
-result = tumopp("-D3 -Chex -N10000 -k1e9 -Lstep -Pmindrag")
+tumopp::tumopp("-h")
+result = tumopp::tumopp("-D3 -Chex -N10000 -k1e9 -Lstep -Pmindrag")
 
 result$population[[1]] |>
-  filter_extant() |>
+  tumopp::filter_extant() |>
   dplyr::filter(z == 0) |>
-  plot_lattice2d()
+  tumopp::plot_lattice2d()
 
 result$population[[1]] |>
-  filter_extant() |>
-  add_surface(result$coord, result$dimensions) |>
+  tumopp::filter_extant() |>
+  tumopp::add_surface(result$coord, result$dimensions) |>
   dplyr::filter(z == 0) |>
   dplyr::filter(surface) |>
-  plot_lattice2d()
+  tumopp::plot_lattice2d()
 
 if (result[["dimensions"]] > 2L) {
-  library(rgl)
-
   rgl::close3d()
   rgl::open3d(windowRect = c(0, 0, 600, 600))
   result$population[[1]] |>
-    filter_extant() |>
-    add_surface(result$coord, result$dimensions) |>
+    tumopp::filter_extant() |>
+    tumopp::add_surface(result$coord, result$dimensions) |>
     dplyr::filter(surface) |>
-    plot_tumor3d()
-  title3d("", "", "x", "y", "z")
+    tumopp::plot_tumor3d()
+  rgl::title3d("", "", "x", "y", "z")
 
-  .outfile = snapshot_surface(result$population[[1]])
+  .outfile = tumopp::snapshot_surface(result$population[[1]])
   system(sprintf("open %s", .outfile))
 
-  writeWebGL(".", "rgl.html", snapshot = FALSE, width = 600, height = 600)
+  rgl::writeWebGL(".", "rgl.html", snapshot = FALSE, width = 600, height = 600)
 } # fi 3D

demo/sample.R

@@ -1,46 +1,43 @@
-library(tidyverse)
-library(tumopp)
-
 # load_all()
 
-(result = tumopp("-N40000 -D2 -Chex -k24 -Lconst"))
+(result = tumopp::tumopp("-N40000 -D2 -Chex -k24 -Lconst"))
 (population = result$population[[1L]])
 (graph = result$graph[[1L]])
-(extant = population |> filter_extant())
+(extant = population |> tumopp::filter_extant())
 
-(regions = sample_uniform_regions(extant, 8L, 100L))
+(regions = tumopp::sample_uniform_regions(extant, 8L, 100L))
 subgraph = tumopp::subtree(graph, unlist(regions$id))
 
 extant |>
   dplyr::left_join(tumopp:::tidy_regions(regions), by = "id") |>
-  plot_lattice2d(size = 0.3) +
-  geom_point(data = function(x) {
+  tumopp::plot_lattice2d(size = 0.3) +
+  ggplot2::geom_point(data = function(x) {
     dplyr::filter(x, !is.na(region))
   }, size = 0.3, alpha = 0.4) +
-  theme(axis.title = element_blank())
+  ggplot2::theme(axis.title = ggplot2::element_blank())
 
 # #######1#########2#########3#########4#########5#########6#########7#########
 
-mutated = mutate_clades(subgraph, mu = 1)
-mutated = mutate_clades(subgraph, mu = -1)
-mutated = mutate_clades(subgraph, segsites = 1000L)
+mutated = tumopp:::mutate_clades(subgraph, mu = 1)
+mutated = tumopp:::mutate_clades(subgraph, mu = -1)
+mutated = tumopp:::mutate_clades(subgraph, segsites = 1000L)
 
-.vaf = make_vaf(subgraph, regions$id, mu = -1) |> print()
+.vaf = tumopp::make_vaf(subgraph, regions$id, mu = -1) |> print()
 .tidy = .vaf |>
-  filter_detectable(0.05) |>
-  sort_vaf() |>
-  longer_vaf() |>
+  tumopp::filter_detectable(0.05) |>
+  tumopp::sort_vaf() |>
+  tumopp::longer_vaf() |>
   print()
 
-.tidy = make_longer_vaf(graph, regions$id, -1) |> print()
-
-ggplot(.tidy) +
-  aes(sample, site) +
-  geom_tile(aes(fill = frequency)) +
-  scale_fill_distiller(palette = "Spectral", limit = c(0, 1), guide = FALSE) +
-  coord_cartesian(expand = FALSE)
+.tidy = tumopp::make_longer_vaf(graph, regions$id, -1) |> print()
 
+ggplot2::ggplot(.tidy) +
+  ggplot2::aes(sample, site) +
+  ggplot2::geom_tile(ggplot2::aes(fill = frequency)) +
+  ggplot2::scale_fill_distiller(palette = "Spectral", limit = c(0, 1), guide = FALSE) +
+  ggplot2::coord_cartesian(expand = FALSE)
 
+ncell = 100L
 testdf = tibble::tibble(mu = rep(c(1, 4, 16, 64), each = 200)) |>
   dplyr::mutate(fst = wtl::mcmap_dbl(mu, \(x) tumopp::make_vaf(subgraph, regions$id, mu = x) |>
     tumopp::dist_vaf(ncell) |>
@@ -51,27 +48,28 @@ testdf = tibble::tibble(mu = rep(c(1, 4, 16, 64), each = 200)) |>
 xi = tumopp::make_vaf(subgraph, regions$id, mu = -1) |>
   tumopp::dist_vaf(ncell) |>
   tumopp::fst()
-ggplot(testdf) +
-  aes(fst) +
-  geom_histogram(bins = 30) +
-  geom_vline(xintercept = xi) +
-  facet_wrap(vars(mu))
+ggplot2::ggplot(testdf) +
+  ggplot2::aes(fst) +
+  ggplot2::geom_histogram(bins = 30) +
+  ggplot2::geom_vline(xintercept = xi) +
+  ggplot2::facet_wrap(ggplot2::vars(mu))
 
 
 # #######1#########2#########3#########4#########5#########6#########7#########
 
-distances = pairwise_distances(subgraph, regions) |> print()
+distances = tumopp::pairwise_distances(subgraph, regions) |> print()
 
 .xmax = max(distances$euclidean)
 .ymax = max(max(distances$fst), 0.6)
 distances |>
-  ggplot(aes(euclidean, fst)) +
-  geom_point() +
-  stat_smooth(method = lm, formula = y ~ x + 0) +
-  coord_cartesian(xlim = c(0, .xmax), ylim = c(0, .ymax))
+  ggplot2::ggplot() +
+  ggplot2::aes(euclidean, fst) +
+  ggplot2::geom_point() +
+  ggplot2::stat_smooth(method = lm, formula = y ~ x + 0) +
+  ggplot2::coord_cartesian(xlim = c(0, .xmax), ylim = c(0, .ymax))
 
-m = dist_genealogy(subgraph, regions[["id"]])
-fst(m)
-gst(m)
+m = tumopp::dist_genealogy(subgraph, regions[["id"]])
+tumopp::fst(m)
+tumopp::gst(m)
 
-w = num_pairs(lengths(regions[["id"]]))
+w = tumopp:::num_pairs(lengths(regions[["id"]]))