David Wilkins wilkox
wilkox
/ pandoc_tinytex.R
Created
September 19, 2023 00:05
Install LaTeX packages for pandoc with tinytex
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| tinytex::tlmgr_install(c("amsfonts", "amsmath", "lm", "unicode-math", "iftex", "listings", "fancyvrb", "longtable", "booktabs", "graphicx", "hyperref", "xcolor", "soul", "geometry", "setspace", "babel", "fontspec", "upquote", "microtype", "csquotes", "natbib", "biblatex", "bibtex", "parskip", "xurl", "bookmark", "footnotehyper", "footnote")) |
wilkox
/ grid_arrange_shared_legend.R
Last active
May 20, 2018 01:45
wilkox
/ create_network_w_edge_weight_new.R
Created
January 18, 2017 10:08
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| # Libraries | |
| library(readr) | |
| library(devtools) | |
| library(SpiecEasi) | |
| library(phyloseq) | |
| library(tibble) | |
| library(igraph) | |
| library(dplyr) | |
| library(stringr) | |
| library(tidyr) |
wilkox
/ create_spiec_network_w_weights.R
Last active
January 16, 2017 03:57
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| # Libraries | |
| library(readr) | |
| library(SpiecEasi) | |
| library(phyloseq) | |
| library(tibble) | |
| library(igraph) | |
| library(dplyr) | |
| library(stringr) | |
| library(tidyr) | |
| library(ggplot2) |
wilkox
/ ggtree_get_ancestors.R
Created
January 2, 2017 03:18
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| # Vectorised version of the private function getAncestor in ggtree | |
| require(ggtree) | |
| get_ancestors <- function(tree, nodes) { | |
| return( | |
| unique( | |
| unlist(lapply(nodes, function(node) ggtree:::getAncestor(tree, node))) | |
| ) | |
| ) | |
| } |
wilkox
/ ggtree_vectorised_expand.R
Created
January 2, 2017 01:13
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| # Vectorised version of ggtree::expand | |
| require(ggtree) | |
| expand_vectorised <- function(tree_view = NULL, nodes) { | |
| if (length(nodes) == 1) { | |
| return(ggtree::expand(tree_view, nodes)) | |
| } else { | |
| return(ggtree::expand( | |
| expand_vectorised(tree_view, nodes[-1]), | |
| nodes[1] | |
| )) |
wilkox
/ ggtree_vectorised_collapse.R
Created
January 2, 2017 01:05
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| # Vectorised version of ggtree::collapse | |
| require(ggtree) | |
| collapse_vectorised <- function(tree_view = NULL, nodes) { | |
| if (length(nodes) == 1) { | |
| return(ggtree::collapse(tree_view, nodes)) | |
| } else { | |
| return(ggtree::collapse( | |
| collapse_vectorised(tree_view, nodes[-1]), | |
| nodes[1] | |
| )) |
wilkox
/ multiplot_file.R
Created
January 1, 2017 01:02
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| multiplot_file <- function(plots = NULL, file, cols = 1, layout = NULL, width = 100, height = 100) { | |
| require(grid) | |
| mm <- function(mm) {return(0.0393701 * mm)} | |
| numPlots = length(plots) | |
| if (is.null(layout)) { | |
| layout <- matrix( | |
| seq(1, cols * ceiling(numPlots/cols)), |
wilkox
/ prepare_SPEIC-EASI.R
Created
September 26, 2016 01:20
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| # Libraries | |
| library(readr) | |
| library(SpiecEasi) | |
| library(phyloseq) | |
| library(tibble) | |
| library(igraph) | |
| library(dplyr) | |
| library(stringr) | |
| library(tidyr) | |
| library(ggplot2) |
wilkox
/ prepare_SPEIC-EASI.R
Created
September 24, 2016 04:13
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| # Libraries | |
| library(readr) | |
| library(SpiecEasi) | |
| library(phyloseq) | |
| library(tibble) | |
| library(igraph) | |
| library(dplyr) | |
| library(stringr) | |
| library(tidyr) | |
| library(ggplot2) |
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