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

Description tinselR modules tinselR functions tinselR utils server functions tinselR module specific functions cladeAnnotator module server functions displayTree module server functions uploadData module server functions uploadData module ui functions located in golem_utils_ui.R file

This is a phylogenetic tree application for annotating trees with additional information. Additional information could come from a genetic distance file or meta data file.

The modules of tinselR are described below:

mod_about - this module generates the landing page for the application and provides a link to the github repo where users may file an issue.

mod_aboutExample - this module generates the tab detailing the example data that is pre-loaded when the application launches.

mod_aboutTreeParams - this module generates the landing page which describes the tree parameters that a user can adjust.

mod_cladeAnnotator - this module allows the user to add or remove annotations and checks for overlap between those annotations and allows the addition of the heatmap. The final annotated tree is sent to the downloadTree module for downloading. This module uses 6 functions: create_tip_list, make_layer, add_map, add_annotations, current_tree_out and snp_anno.

mod_displayTree - this module combines the tree with genetic distance that allows tree plotting and accessing the combined genetic data for adding annotations. This module uses 2 functions: tree_plot and combine_g_and_t.

mod_exampleData - this module sources the pre-loaded example data (e.g. tree (x3), genetic distance file (x3), and meta data file (x3)), which are already combined as a dataset (e.g. example data 1 is the combined data files of example tree 1, example genetic 1, and example meta 1). This module uses 3 functions: replace_column_header, gene_object_out, m_file_conversion.

mod_FAQ - this module generates the tab for a frequently asked questions section.

mod_paramsTree - this module holds all of the parameters that can be adjusted for the phylogenetic tree and ultimately are passed to either the displayTree or cladeAnnotator module.

mod_pushButtons - this module generates the action buttons for adding a tree, adding/removing a tree, or adding/removing a heatmap.

mod_relaunchApp - this module will relaunch the entire application and clear out any exisiting tree images that are plotted.

mod_tipCheck - this module generates messages for the user regarding the files uploaded and if column(s) for a heatmap is available. This module uses 3 functions: sanity, not_columns, and m_file_conversion.

mod_uploadData - this module allows the user to upload three different types of files and does file checking to confirm the correct delimiter is selected. The output from this module is sent to three different modules (tipCheck, displayTree, and cladeAnnotator). This module uses 5 server functions: read_data, file_type, file_check, replace_column_header, gene_object_out. This module uses 2 ui functions: file_upload and input_separator.

The functions of tinselR are described below:

The functions that are shared between modules or unit testing are included in file called goelm_utils_server.R We describe those functions below and indicated where these functions are called.

sanity - Inputs: m_file, g_file, t_file - which are the three different file types a user can upload and are imported (meta, file, genetic distance file, and a tree file). g_file class - spec_tbl_df, tbl_df, tbl, data.frame; m_file class - spec_tbl_df, tbl_df, tbl, data.frame; t_file class - phylo. Output: ui displayed messages indicating if the files are concordant in tip labels and informing the user where an inconsistency is in tip labels for the three files. Used in tipcheck module and unit tests.

not_columns - Input: file - this file is the meta data file that has been converted using the function m_file conversion. file class - spec_tbl_df, tbl_df, tbl, data.frame. Output: ui displayed message that tells user if there is a column included that allows the user to add a heatmap. Used in tipcheck module and unit tests.

replace_column_header - Inputs: gene_file_in - this is the genetic distance file which is imported. gene_file_in class - spec_tbl_df, tbl_df, tbl, data.frame. Output: spec_tbl_df, tbl_df, tbl, data.frame with row 1, column 1 changed to 'label', which is done for joining this file with the tree file. Used in uploadData and exampleData module.

gene_object_out - Inputs: gene_file_in - this is the genetic distance file which is imported. gene_file_in class - spec_tbl_df, tbl_df, tbl, data.frame. Output: spec_tbl_df, tbl_df, tbl, data.frame. Essentially, this converts the matrix to a three column data frame (isolate 1, isolate 2, and pairwise snp differences between them). It also removes rows with na and self comparisons as that would skew the calculation of mean snps. Used in uploadData and exampleData module.

m_file_conversion - Input: m_file - this file is the meta data file that has been converted using the function m_file conversion. m_file class - spec_tbl_df, tbl_df, tbl, data.frame. Output: meta data file with converted tips labels to row names and the removal of the original tip labels that you a user is correcting for. used in tipCheck and exampleData modules.

combine_g_and_t - Inputs: tree_file and gene_file - these files are used to be combined by the shared id of label. gene_file class - spec_tbl_df, tbl_df, tbl, data.frame; t_file class - phylo. Output - a tibble that will be converted to a treedata object. Used in displayData module and unit tests.

snp_anno - Inputs: gene_file and tips - gene_file is the converted three column genetic distance file; while the tips input all user selected tips. gene_file class - spec_tbl_df, tbl_df, tbl, data.frame; tips class - list. Output: is a numeric vector of snp differences for the selection of highlighted tips. Used in the cladeAnnotator module and unit tests.

The functions that are only used in specific modules are defined in those modules. We describe those functions below and indicated the modules these functions are associated with.

create_tip_list - Inputs: none. Output: is a list with incremented counts associated with a user selection or brushed tips.

make_layer - Inputs: tree, tips, label, color, offset - tree is a treedata object, tips - user selected tips, label - determines the node for where the annotation is drawn and is used subsequently to calculate the median and range of snps in the add_annotation function, color - user determined color of the label, offset - user determined offset from the tip labels. Output: ultimately remembers all layers that need to be added to a phylogenetic tree.

add_map - Inputs: tree, metaFile - tree is a treedata object, metaFile is of class - spec_tbl_df, tbl_df, tbl, data.frame after converting the meta data file. Output: is a column for the heatmap color coded by the data within the column (e.g. source site data colored by collection source).

add_annotations - Inputs: tree_plot and tip_vector_in - tree_plot is a treedata object while tip_vector_in uses the function create_tip_list to known which tips have been selected. This function determines if there are overlapping tip labels in user selected tips. If so, then adjusts the placement of the annotation. Additionally, this function relies on the make_layer function to determine the placement of drawn on annotations and adds the median and range of snps for annotations.

current_tree_out - Inputs: none. Outputs - tree which includes the added heatmap if avaiable, added annotations if selected.

tree_plot - Input: either a tree of class phylo if no genetic data uploaded or a treedata object. Output: tree of class ggtree, gg, ggplot.

read_data - Inputs: file_path and sep. file_path is the path to the location of the file you are interested in uploading, while sep is the delimiter for the selected file, which can be a comma or tab. Output: is an imported file for genetic distance and/or meta data file.

file_type - Inputs: in_var is the input delimiter for the file uploaded. Output: returns either a comma or a tab, which is used in file_check function to determine if the correct delimiter has be selected.

file_check - Inputs: file_up, file_type, file_sep - file_up is the file a user has uploaded, file_type is the mapped type of delimiter, file_sep is the user selected separator used in the read_data function. Output: ui displayed message which confirms if user has selected the corrector delimiter for the files they uploaded.

file_upload - Inputs: file_id and file_label - file_id is the assigned id to the file, while file_label is the label assigned to the file and is visible in the ui. Outputs: Ultimately the uploaded file type can be of text, csv, or txt format.

input_separator - Inputs: file_id and file_label - file_id is the assigned id to the file, while file_label is the label assigned to the file and is visible in the ui. Output is the type of file format can either be tab or comma.

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