mod_displayTree: mod_displayTree_ui and mod_displayTree_server

In jennahamlin/Tinsel: An R Shiny Application for annotating outbreak phylogenetic trees

Description

A shiny Module. This module combines the tree with genetic distance as an tidytree object that allows tree plotting and accessing the combined data. This module contains 1 function at the end of the script that is used within (tree_plot). The tree_plot function allows for various parameters to be changed dynaically on the tree image. This module also uses one function in the golem_utils_server file (combine_g_and_t), which combines the tree and genetic distance matrix that has already been transformed with the meta data file.

Usage

mod_displayTree_ui(id)

mod_displayTree_server(
  input,
  output,
  session,
  tree_file_out,
  geneObjectOutForSNP,
  align,
  tree_format,
  font,
  num_scale,
  node,
  lim,
  boot_pos,
  mid_p,
  mat_off
)

Arguments

id	shiny id
input	internal
output	internal
session	internal
tree_file_out	- from upload/example Data module. class of phylo
geneObjectOutForSNP	- from upload/example Data module. class of "spec_tbl_df", "tbl_df", "tbl", and "data.frame" #' @param align - from paramsTree module; this is checkbox input (Y or N)
tree_format	- from paramsTree module; checkbox input (multiple choice)
font	- from paramsTree module; checkbox input (multiple choice)
num_scale	- from paramsTree module; this is numeric input from user
node	- from paramsTree module; this is numeric input from user
lim	- from paramsTree module; this is numeric input from user
boot_pos	- from paramsTree module; this is numeric input from user
mid_p	- from paramsTree module; this is checkbox input (Y or N)
mat_off	- from paramsTree module; this is numeric input from user

Details

displayTree Function

jennahamlin/Tinsel documentation built on Sept. 15, 2021, 9:46 a.m.