mod_cladeAnnotator: mod_cladeAnnotator_ui and mod_cladeAnnotator_server

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

Description

A shiny Module. This module allows the user to add or remove annotations and checks for overlap between those annotations and allows the addition of the heatmap. This module contains 5 functions at the end of the script that are used within (create_tip_list, make_layer, add_map, add_annotations, and current_tree_out). These functions allow the placement of annotations for all selected tips. This module also contains one function in the golem_utils_server file (snp_anno), which gets the snps for the selected tips.

Usage

mod_cladeAnnotator_ui(id)

mod_cladeAnnotator_server(
  input,
  output,
  session,
  mFileMatOut,
  make_tree_out,
  add_tree,
  add_anno,
  remove_anno,
  add_heatmap,
  remove_heatmap,
  geneObjectForSNP,
  label_off,
  lab_color,
  mat_off,
  heat_col,
  anno_text,
  median_text
)

Arguments

id	shiny id
input	internal
output	internal
session	internal
mFileMatOut	- from dataDisplay module; is a dataframe
make_tree_out	- from dataDisplay module; class of ggtree, gg, ggplot2
add_tree	- from pushButtons module; is an action button (Y or N)
add_anno	- from pushButtons module; is an action button (Y or N)
remove_anno	- from pushButtons module; is an action button (Y or N)
add_heatmap	- from pushButtons module; is an action button (Y or N)
remove_heatmap	- from pushButtons module; is an action button (Y or N)
geneObjectForSNP	- from upload/example Data module. Is a tibble
lab_color	- from paramsTree; select input from user (multiple choice)
mat_off	- from paramsTree module; this is numeric input from user
anno_text	- from paramsTree; user input text (blank or any word)
median_text	- from paramsTree; user input text (blank or any word)
label_off-	from paramsTree module; this is numeric input from user
heat_color	- from paramsTree; select input from user (multiple choice)

Details

cladeAnnotator Function

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