Skip to contents

Annotate

Source: R/fct_Annotate.R
Annotate.Rd

R6 class object used for generating and storing plots and other processed data. It is accessed internally to display data. Each top level list contains a different type of plot. Sublists are organised to store different plot versions. Functions for plotting (i.e. plot_actogram, plot_DAct) get data from fct_R6_Custom_tables object and generate a plot that is saved into the relative list. There should be a method to pass plots to an external container based on the handler.

Value

An Annotate object

Public fields

store

named list used as a keyed registry for all plot objects. Use store_obj(key, object) and retrieve_obj(key) to read and write. Keys used in the app: "ts_original", "ts_annotated", "periodogram_total", "periodogram_faceted", "periodogram_averaged", "period_barplot".

actTable

Table containing data assembled using showData()

metaTable

Table containing data assembled using showMeta() showMeta

Methods

Public methods

Method showMeta()

function to create a table that arranges all the available metadata in a table, and saves it in metaTable var

Usage

Annotate$showMeta(env)

Arguments

env

App_settings environment to access myCleanMice object

Returns

no return showdata

Method showData()

function to create a table that arranges activity data in a table, and saves it in actTable var

Usage

Annotate$showData(env, id, miceList)

Arguments

env

App_settings environment to access myCleanMice object

id

mouse Id value from the list of Ids or "All" to display all data

miceList

list of all available mouse Ids

Returns

no return store_obj

Method store_obj()

a function to store objects inside the Annotate R6 obj

Usage

Annotate$store_obj(key, object)

Arguments

key

string to discriminate cases for storing file

object

the object to be stored

Returns

no value returned retrieve_obj

Method retrieve_obj()

retrieve a stored object by key

Usage

Annotate$retrieve_obj(key)

Arguments

key

string key used when storing the object

Returns

the stored object, or NULL if the key does not exist plot_Timeserie

Method plot_Timeserie()

a function to create Timeseries plots

Usage

Annotate$plot_Timeserie(
  datatable,
  value,
  env,
  tmin = 0,
  tmax = 999.81,
  data1 = TRUE,
  data2 = FALSE,
  data3 = FALSE,
  timeformat = "Hours"
)

Arguments

datatable

list contain all the data

value

string to select data source: original, detrended or cleaned

env

environment. App settings environment

tmin

double. minimum time to be plotted

tmax

double. maximum time to be plotted

data1

Boolean. is dataset 1 present?

data2

Boolean. is dataset 2 present?

data3

Boolean. is dataset 3 present?

timeformat

String. is the time in hours or posixt

Returns

a ggplot object plot_Timeserie_facet

Method plot_Timeserie_facet()

a function to create Timeseries plots stacked inside a grid

Usage

Annotate$plot_Timeserie_facet(
  datalist,
  value,
  env,
  tmin = 0,
  tmax = 999.81,
  data1 = TRUE,
  data2 = FALSE,
  data3 = FALSE,
  timeformat = "Hours"
)

Arguments

datalist

list contain all the data

value

string to select data source: original, detrended or cleaned

env

environment. App settings environment

tmin

double. minimum time to be plotted

tmax

double. maximum time to be plotted

data1

Boolean. is dataset 1 present?

data2

Boolean. is dataset 2 present?

data3

Boolean. is dataset 3 present?

timeformat

String. is the time in hours or posixt

Returns

a ggplot object plot_periodogram

Method plot_periodogram()

Function to generate periodogram plots

Usage

Annotate$plot_periodogram(
  method,
  plotType = c("Pertotal", "Perfaceted", "Peraveraged"),
  FunEnv
)

Arguments

method

function to use from zeitgebr::periodogram function

plotType

the different type of plots to generate. default to total and faceted

FunEnv

AppSettings environment

Returns

function returns internally, no direct output

plot_period_barplot

Method plot_period_barplot()

Usage

Annotate$plot_period_barplot(method, FunEnv)

Arguments

method

function used to run period analysis

FunEnv

AppSettings environment

Returns

function returns internally

Method clone()

The objects of this class are cloneable with this method.

Usage

Annotate$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.