initial commit

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

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+Package: dynmethods
+Type: Package
+Title: Wrappers for trajectory inference methods
+Version: 0.1.0
+Authors@R: c(
+  person("Robrecht", "Cannoodt", email = "[email protected]", role = c("aut", "cre")),
+  person("Wouter", "Saelens", email = "[email protected]", role = c("aut")),
+  person("Helena", "Todorov", email = "[email protected]", role = c("aut")))
+Description: dynmethods provides wrappers for TI methods and their respective plotting functions.
+License: GPL-3
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 6.0.1
+Depends:
+  R (>= 3.4.0)
+Imports: 
+  coRanking,
+  cowplot,
+  dplyr, 
+  dynplot,
+  dynutils,
+  GA,
+  GEDEVO,
+  ggforce,
+  ggplot2,
+  grDevices,
+  grid,
+  igraph,
+  jsonlite,
+  magrittr, 
+  methods,
+  mlr,
+  mlrMBO,
+  netdist,
+  parallelMap,
+  ParamHelpers,
+  pbapply,
+  pdist,
+  pheatmap,
+  PRISM,
+  purrr, 
+  randomForest,
+  RColorBrewer,
+  readr,
+  reshape2,
+  smoof,
+  stringr,
+  testthat,
+  tibble, 
+  tidyr,
+  viridis,
+  vegan
+Suggests:
+  Biobase,
+  BiocGenerics,
+  cellTree,
+  coda,
+  destiny,
+  diffusionMap,
+  dyntoy,
+  embeddr,
+  fastICA,
+  GPfates,
+  lle,
+  MASS,
+  Matrix,
+  Mpath,
+  mfa,
+  monocle,
+  ouija,
+  phenopath,
+  pseudogp,
+  Rtsne,
+  rstan,
+  roxygen2,
+  scater,
+  SCORPIUS,
+  SCOUP,
+  SCUBA,
+  SLICE,
+  SLICER,
+  slingshot,
+  StemID,
+  topslam,
+  TSCAN,
+  Waterfall,
+  Wishbone,
+  MCMCglmm
+Remotes:
+  alan-turing-institute/network-comparison,
+  berndbischl/ParamHelpers@dd54fe2719492dc0a03c6fe277d6ccaf255f6200,
+  bioc::Biobase,
+  bioc::BiocGenerics,
+  bioc::cellTree,
+  bioc::destiny,
+  bioc::scater,
+  bioc::TSCAN,
+  dynverse/GEDEVO,
+  dynverse/GPfates,
+  dynverse/monocle,
+  dynverse/Mpath,
+  dynverse/SCOUP,
+  dynverse/SCUBA,
+  dynverse/SLICE,
+  dynverse/SLICER,
+  dynverse/StemID,
+  dynverse/topslam,
+  dynverse/Waterfall,
+  dynverse/Wishbone,
+  kieranrcampbell/pseudogp,
+  kieranrcampbell/embeddr,
+  kieranrcampbell/mfa,
+  kieranrcampbell/ouija,
+  kieranrcampbell/phenopath,
+  kstreet13/slingshot,
+  mlr-org/mlr,
+  rcannood/dynutils,
+  rcannood/PRISM,
+  rcannood/SCORPIUS,
+  Zouter/dynplot,
+  Zouter/dyntoy
+

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(check_dependencies)
+export(description_celltree_gibbs)
+export(description_celltree_maptpx)
+export(description_celltree_vem)
+export(description_dpt)
+export(description_embeddr)
+export(description_gpfates)
+export(description_identity)
+export(description_mfa)
+export(description_monocle1_ica)
+export(description_monocle2_ddrtree)
+export(description_mpath)
+export(description_ouija)
+export(description_phenopath)
+export(description_pseudogp)
+export(description_random)
+export(description_scorpius)
+export(description_scoup)
+export(description_scuba)
+export(description_shuffle)
+export(description_slice)
+export(description_slicer)
+export(description_slingshot)
+export(description_stemid)
+export(description_topslam)
+export(description_tscan)
+export(description_waterfall)
+export(description_wishbone)
+export(execute_method)
+export(execute_method_internal)
+export(get_descriptions)
+import(ParamHelpers)
+import(dplyr)
+import(dynutils)
+import(ggplot2)
+import(methods)
+import(tibble)
+import(tidyr)
+importFrom(RColorBrewer,brewer.pal)
+importFrom(cowplot,plot_grid)
+importFrom(dplyr,bind_cols)
+importFrom(dynplot,process_dynplot)
+importFrom(ggforce,geom_arc_bar)
+importFrom(grDevices,colorRampPalette)
+importFrom(grDevices,rainbow)
+importFrom(grid,arrow)
+importFrom(igraph,degree)
+importFrom(igraph,distances)
+importFrom(igraph,get.vertex.attribute)
+importFrom(igraph,induced_subgraph)
+importFrom(magrittr,"%$%")
+importFrom(magrittr,"%<>%")
+importFrom(magrittr,set_colnames)
+importFrom(pdist,pdist)
+importFrom(purrr,"%>%")
+importFrom(purrr,discard)
+importFrom(purrr,keep)
+importFrom(purrr,map)
+importFrom(purrr,map_chr)
+importFrom(purrr,map_dbl)
+importFrom(purrr,map_df)
+importFrom(purrr,map_int)
+importFrom(purrr,map_lgl)
+importFrom(purrr,set_names)
+importFrom(readr,read_csv)
+importFrom(readr,read_file)
+importFrom(readr,write_file)
+importFrom(reshape2,melt)
+importFrom(stats,cor)
+importFrom(stats,dist)
+importFrom(stats,kmeans)
+importFrom(stats,median)
+importFrom(stats,na.omit)
+importFrom(stats,prcomp)
+importFrom(stats,quantile)
+importFrom(stats,runif)
+importFrom(stats,setNames)
+importFrom(stats,step)
+importFrom(stats,time)
+importFrom(stats,var)
+importFrom(stringr,str_length)
+importFrom(utils,capture.output)
+importFrom(utils,head)
+importFrom(utils,installed.packages)
+importFrom(utils,lsf.str)
+importFrom(utils,read.table)
+importFrom(utils,tail)
+importFrom(utils,write.table)
+importFrom(viridis,scale_colour_viridis)

R/helper_dimred_expr.R

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+list_dimred_methods <- function() {
+  list(
+    pca = dimred_pca,
+    mds = dimred_mds,
+    tsne = dimred_tsne,
+    ica = dimred_ica,
+    lle = dimred_lle
+  )
+}
+
+dimred <- function(x, method, ...) {
+  methods <- list_dimred_methods()
+  if (method %in% names(methods)) {
+    meth <- methods[[method]]
+    params <- list(x = x, ...)
+    do.call(meth, params)
+  } else {
+    stop("Method ", sQuote(method), " not found.")
+  }
+}
+
+process_dimred <- function(space, rn) {
+  space <- as.matrix(space)
+  dimnames(space) <- list(rn, paste0("Comp", seq_len(ncol(space))))
+  space
+}
+
+
+dimred_pca <- function(x, ndim = 3) {
+  space <- prcomp(t(x))$rotation[,seq_len(ndim)]
+  process_dimred(space, rownames(x))
+}
+
+dimred_mds <- function(x, ndim = 3) {
+  requireNamespace("SCORPIUS")
+  space <- SCORPIUS::reduce_dimensionality(SCORPIUS::correlation_distance(x), ndim = ndim)
+  process_dimred(space, rownames(x))
+}
+
+dimred_tsne <- function(x, ndim = 3) {
+  requireNamespace("SCORPIUS")
+  requireNamespace("Rtsne")
+  requireNamespace("stats")
+  space <- Rtsne::Rtsne(stats::as.dist(SCORPIUS::correlation_distance(x)), dims = ndim, is_distance = TRUE)$Y
+  process_dimred(space, rownames(x))
+}
+
+dimred_ica <- function(x, ndim = 3) {
+  requireNamespace("fastICA")
+  space <- fastICA::fastICA(t(scale(t(x))), ndim)$S
+  process_dimred(space, rownames(x))
+}
+
+dimred_lle <- function(x, ndim = 3) {
+  requireNamespace("lle")
+  poss_k <- lle::calc_k(t(scale(t(x))), ndim)
+  k <- poss_k$k[which.min(poss_k$rho)]
+  space <- lle::lle(t(scale(t(x))), ndim, k)$Y
+  process_dimred(space, rownames(x))
+}

R/helper_project_trajectory.R

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+#' @importFrom pdist pdist
+project_cells_to_segments <- function(
+  cluster_network,
+  cluster_space,
+  sample_space,
+  sample_cluster,
+  num_segments_per_edge = 100,
+  milestone_rename_fun = NULL
+) {
+  # collect information on cells
+  space_df <- sample_space %>%
+    as.data.frame %>%
+    rownames_to_column("cell_id") %>%
+    mutate(label = sample_cluster)
+
+  # collect information on clusters
+  centers_df <- cluster_space %>%
+    as.data.frame %>%
+    rownames_to_column("clus_id")
+
+  # collect information on edges
+  edge_df <- cluster_network %>%
+    left_join(centers_df %>% rename(from = clus_id) %>% rename_if(is.numeric, function(x) paste0("from.", x)), by = "from") %>%
+    left_join(centers_df %>% rename(to = clus_id) %>% rename_if(is.numeric, function(x) paste0("to.", x)), by = "to")
+
+  # construct segments
+  segment_df <- edge_df %>%
+    rowwise() %>%
+    do(data.frame(
+      from = .$from,
+      to = .$to,
+      percentage = seq(0, 1, length.out = num_segments_per_edge),
+      sapply(colnames(sample_space), function(x) {
+        seq(.[[paste0("from.", x)]], .[[paste0("to.", x)]], length.out = num_segments_per_edge)
+      }),
+      stringsAsFactors = FALSE
+    )) %>%
+    ungroup()
+
+  # calculate shortest segment piece for each cell
+  segment_ix <- sapply(seq_len(nrow(sample_space)), function(i) {
+    x <- sample_space[i,]
+    la <- space_df$label[[i]]
+    ix <- which(segment_df$from == la | segment_df$to == la)
+    dis <- pdist::pdist(x, segment_df[ix,colnames(sample_space)])
+    wm <- which.min(as.matrix(dis)[1,])
+    ix[wm]
+  })
+
+  # construct progressions
+  progressions <- data.frame(
+    cell_id = rownames(sample_space),
+    segment_df[segment_ix,] %>% select(from, to, percentage),
+    stringsAsFactors = TRUE
+  )
+
+  # collect milestone network and ids
+  milestone_network <- edge_df %>%
+    select(from, to, length, directed)
+  milestone_ids <- rownames(cluster_space)
+
+  # rename milestones
+  if (!is.null(milestone_rename_fun)) {
+    progressions <- progressions %>% mutate_at(c("from", "to"), milestone_rename_fun)
+    milestone_network <- milestone_network %>% mutate_at(c("from", "to"), milestone_rename_fun)
+    milestone_ids <- milestone_rename_fun(milestone_ids)
+    edge_df <- edge_df %>% mutate_at(c("from", "to"), milestone_rename_fun)
+    centers_df <- centers_df %>% mutate(clus_id = milestone_rename_fun(clus_id))
+    space_df <- space_df %>% mutate(label = milestone_rename_fun(label))
+  }
+
+  lst(
+    milestone_ids,
+    milestone_network,
+    progressions,
+    space_df,
+    centers_df,
+    edge_df
+  )
+}

R/package.R

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+#' Wrappers for trajectory inference methods
+#'
+#' @import dplyr
+#' @import tidyr
+#' @import methods
+#' @import ParamHelpers
+#' @import tibble
+#' @import ggplot2
+#' @import dynutils
+#' @importFrom dynplot process_dynplot
+#' @importFrom stats cor dist kmeans median prcomp quantile runif setNames step time
+#' @importFrom utils installed.packages head tail
+#' @importFrom purrr %>% map map_df map_chr map_lgl map_int map_dbl keep discard set_names
+#' @importFrom magrittr %<>% %$%
+#'
+#' @docType package
+#' @name dyneval
+NULL