Title: Explore Temporal and Other Phylogenetic Signals
Version: 0.0.8
Description: Sequences sampled at different time points can be used to infer molecular phylogenies on natural time scales, but if the sequences records inaccurate sampling times, that are not the actual sampling times, then it will affect the molecular phylogenetic analysis. This shiny application helps exploring temporal characteristics of the evolutionary trees through linear regression analysis and with the ability to identify and remove incorrect labels. The method was extended to support exploring other phylogenetic signals under strict and relaxed models.
License: GPL-3
Depends: R (≥ 3.3.0)
Imports: ape, forecast, ggplot2, ggprism, ggpmisc, ggtree, golem (≥ 0.3.1), shiny (≥ 1.6.0), shinydashboard, shinyjs, shinyWidgets, stats, treeio, yulab.utils (≥ 0.1.4), nlme
Suggests: attempt, conflicted, config (≥ 0.3.1), glue, htmltools, knitr, prettydoc, processx, rmarkdown, testthat (≥ 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
RoxygenNote: 7.3.1
Config/testthat/edition: 3
URL: https://github.com/YuLab-SMU/shinyTempSignal, https://www.sciencedirect.com/science/article/pii/S167385272400033X
BugReports: https://github.com/YuLab-SMU/shinyTempSignal/issues
NeedsCompilation: no
Packaged: 2024-03-06 07:47:21 UTC; HUAWEI
Author: Guangchuang Yu ORCID iD [aut, cre, cph], Xiao Luo [ctb], Li Zhan [ctb], Xuanan Zhu [ctb], Jianfeng Lin [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-06 08:00:02 UTC

shinyTempSignal: Explore Temporal and Other Phylogenetic Signals

Description

Sequences sampled at different time points can be used to infer molecular phylogenies on natural time scales, but if the sequences records inaccurate sampling times, that are not the actual sampling times, then it will affect the molecular phylogenetic analysis. This shiny application helps exploring temporal characteristics of the evolutionary trees through linear regression analysis and with the ability to identify and remove incorrect labels. The method was extended to support exploring other phylogenetic signals under strict and relaxed models.

Author(s)

Maintainer: Guangchuang Yu guangchuangyu@gmail.com (ORCID) [copyright holder]

Other contributors:

See Also

Useful links:

Example data: a tree of 76 H3 hemagglutinin gene sequences of a lineage containing swine and human influenza A viruses

Description

This example data was reported on Liang et al. 2014

Format

a tree with 76 sequences

Value

a tree, phylo

Examples

data(MCC_FluA_H3_tree)

The application server-side

Description

The application server-side

Usage

app_server(input, output, session)

Arguments

input

Internal parameter

output

Internal parameter

session

Internal parameter

The application User-Interface

Description

The application User-Interface

Usage

app_ui(request)

Arguments

request

Internal parameter

Convert dates according to date format

Description

Convert dates according to date format

Usage

dateNumeric(date, format)

Arguments

date

input a data extracted from labels, character

format

input format of the date, character

Value

Returns a date of numeric type, numeric

Examples


dateNumeric(date = "1999-12-07", format = "yyyy-MM-dd")

Run the Shiny Application

Description

Run the Shiny Application

Usage

run_shinyTempSignal(
  onStart = NULL,
  options = list(),
  enableBookmarking = NULL,
  uiPattern = "/",
  ...
)

Arguments

onStart

A function that will be called before the app is actually run. This is only needed for shinyAppObj, since in the shinyAppDir case, a global.R file can be used for this purpose.

options

Named options that should be passed to the runApp call (these can be any of the following: "port", "launch.browser", "host", "quiet", "display.mode" and "test.mode"). You can also specify width and height parameters which provide a hint to the embedding environment about the ideal height/width for the app.

enableBookmarking

Can be one of "url", "server", or "disable". The default value, NULL, will respect the setting from any previous calls to enableBookmarking(). See enableBookmarking() for more information on bookmarking your app.

uiPattern

A regular expression that will be applied to each GET request to determine whether the ui should be used to handle the request. Note that the entire request path must match the regular expression in order for the match to be considered successful.

...

arguments to pass to golem_opts. See '?golem::get_golem_options' for more details.

Value

Shiny application object

Examples

if (interactive()) {
  run_shinyTempSignal()
}

shinyTempSignal_set_theme

Description

set default theme

Usage

shinyTempSignal_set_theme(theme)

Arguments

theme

a ggplot theme

Value

No value return