Package 'LifemapR'

Title: Data Visualisation on 'Lifemap' Tree
Description: Allow to visualise data on the NCBI phylogenetic tree as presented in Lifemap <http://lifemap.univ-lyon1.fr/>. It takes as input a dataframe with at least a "taxid" column containing NCBI format TaxIds and allows to draw multiple layers with different visualisation tools.
Authors: Cassandra Bompard [aut], Damien M. de Vienne [aut], Aurélie Siberchicot [ctb, cre]
Maintainer: Aurélie Siberchicot <[email protected]>
License: MIT + file LICENSE
Version: 1.1.4
Built: 2024-09-13 05:10:27 UTC
Source: https://github.com/lifemap-tol/lifemapr

Help Index

Add a graphical element to a tree visualisation.

Description

Add a graphical element to a tree visualisation.

Usage

## S3 method for class 'lifemap_obj'
e1 + e2

Arguments

e1

An object of class lifemap_obj that contains at least $df, a dataframe, and $basemap, the map used to get the coordinates.
e2

A description of the graphical features wanted for a set of points (eg. markers, subtree, piecharts, ...).

Value

A lifemap_obj object.

Examples

## Only run examples in interactive R sessions
if (interactive()) {
data(LM_eukaryotes)
LM_obj <- lifemap(LM_eukaryotes) + lm_markers() + lm_branches()
}

Compute the aesthetics for a subtree visualisation.

Description

Compute the aesthetics for a subtree visualisation.

Usage

add_lm_branches(
  proxy,
  aes,
  df,
  df_visible,
  df_descendants,
  group_info,
  all_taxids
)

Arguments

proxy

The map to be modified.
aes

The dataframe containing the aesthetics details (must be of lm_branches class).
df

The full dataframe.
df_visible

The dataframe containing visible taxa.
df_descendants

The dataframe containing all the information on the descendants of visible taxa.
group_info

the ID of this group of lines.
all_taxids

A vector containing all the visible taxids and their direct descendants.

Value

An updated map with the new layer added.

Compute the aesthetics for markers visualisation.

Description

Compute the aesthetics for markers visualisation.

Usage

add_lm_markers(proxy, aes, df, df_visible, group_info)

Arguments

proxy

The map to be modified.
aes

The dataframe containing the aesthetics information (must be of lm_markers class).
df

The full dataframe.
df_visible

The dataframe containing visible taxa.
group_info

The ID of this group of markers.

Value

An updated map with the new layer added.

Compute the aesthetics for discret values visualisation.

Description

Compute the aesthetics for discret values visualisation.

Usage

add_lm_piecharts(proxy, aes, df, df_visible, layer)

Arguments

proxy

The map to be modified.
aes

The dataframe containing the aesthetics details (must be of lm_piecharts class).
df

The full dataframe.
df_visible

The dataframe containing visible taxa.
layer

The ID of this group of charts

Value

An updated map with the new layer added.

A function to construct a LifemapR object, usable by the other functions of the package.

Description

A function to construct a LifemapR object, usable by the other functions of the package.

Usage

build_Lifemap(df, basemap = c("ncbi", "base", "fr", "virus"), verbose = TRUE)

Arguments

df

A dataframe containing at least one column named "taxid" that contains NCBI Taxonomy Identifiers (taxid). The dataframe can contain any number of additional columns defining traits/characters/values associated to each taxid.
basemap

The chosen basemap for Lifemap ("fr", "ncbi", "base" or "virus").
verbose

If TRUE (the default), the function will print detailed information to the console. If FALSE, it will run silently.

Value

A list of class lifemap_obj containing:

  • df : a dataframe containing at least for each taxid :

    • The x coordinate (lon)

    • The y coordonate (lat)

    • The scientific name (sci_name)

    • The zoom level at which the taxa is visible (zoom)

    • A list of its ascendants (ascend)

    • Its type ("requested" or "ancestor")

    • Its direct ancestor

    • Its type (type), i.e. whether the taxid was requested by the user ("requested") or if it is the anecestor of a requested taxid ("ancestor")

  • basemap : the basemap used to get taxa's details

Examples

data(eukaryotes_80)
## Not run: 
# make sure you have a good internet connection to load these very large files
LM <- build_Lifemap(eukaryotes_80, "fr")

## End(Not run)

Create a dataframe for the ancestry.

Description

Create a dataframe with pairs of taxids, each taxid and their corresponding values are associated with every one of its ancestors.

Usage

create_matrix(df, cols)

Arguments

df

A dataframe containing taxids and values.
cols

The columns containing the values which needs to be inferred.

Value

A dataframe.

Examples

data(LM_eukaryotes)

create_matrix(LM_eukaryotes$df, c("GC.", "Genes"))

Compute a new scale for a value

Description

Compute a new scale for a value

Usage

create_value_range(value, df, df2, min, max)

Arguments

value

A vector of values.
df

The full dataframe.
df2

The dataframe containing visibles taxa.
min

The new minimum of the range.
max

The new maximum of the range.

Value

A vector of values.

Create a Lifemap base.

Description

This function create a blank Leaflet map using the leaflet function from the leaflet package. If a dataframe is provided, it will be used for the creation of the map.

Usage

display_map(df = NULL, basemap = c("fr", "ncbi", "base", "virus"))

Arguments

df

A dataframe. If given, its columns can be easily accessed with "~" (eg. ~GC.).
basemap

The basemap choosen to be displayed, it can be either :

Value

An HTML widget object with graphics layers.

Examples

display_map()

Compute the different display options.

Description

Compute the different display options.

Usage

display_option(m, aes, df, type, leaves, i)

Arguments

m

The map to be modified.
aes

The dataframe containing the aesthetics details
df

The full dataframe.
type

A string indicating the type of representation, either "markers" or "discret"
leaves

The Vector of all the terminal taxids.
i

The index of the aesthetics.

Value

An updated map.

Represent data on a Lifemap basemap.

Description

Draw a map and all the aesthetics in the order you put them in, the last one will be on top of the others.

Usage

draw_Lifemap(lm_obj)

Arguments

lm_obj

A Lifemap object filled with aesthetics.

Value

A shiny application

Examples

## Only run examples in interactive R sessions
if (interactive()) {
data(LM_eukaryotes)
lifemap(LM_eukaryotes) + lm_markers() + lm_branches()
}

NCBI information for 1000 eukaryotes

Description

A dataset containing NCBI information of 1000 eukaryotes. The variables are as follows:

Usage

data(eukaryotes_1000)

Format

A data frame with 1000 rows and 19 variables:

X.Organism.Name

Organism name at the species level

taxid

NCBI taxid

BioProject.Accession

BioProject Accession number (from BioProject database)

BioProject.ID

BioProject ID

Group

Commonly used organism groups: Animals, Fungi, Plants, Protists

SubGroup

NCBI Taxonomy level below group: Mammals, Birds, Fishes, Flatworms, Insects, Amphibians, Reptiles, Roundworms, Ascomycetes, Basidiomycetes, Land Plants, Green Algae, Apicomplexans, Kinetoplasts

Size..Mb.

Total length of DNA submitted for the project

GC.

Percent of nitrogenous bases (guanine or cytosine) in DNA submitted for the project

Assembly.Accession

Name of the genome assembly (from NCBI Assembly database)

Replicons

Number of replicons in the assembly

WGS

Four-letter Accession prefix followed by version as defined in WGS division of GenBank/INSDC

Scaffolds

Number of scaffolds in the assembly

Genes

Number of Genes annotated in the assembly

Proteins

Number of Proteins annotated in the assembly

Release.Date

First public sequence release for the project

Modify.Date

Sequence modification date for the project

Status

Highest level of assembly:
Chromosomes: one or more chromosomes are assembled
Scaffolds or contigs: sequence assembled but no chromosomes

Center

Origin of the sample

BioSample.Accession

BioSample Accession number

NCBI information for 80 eukaryotes

Description

A dataset containing NCBI information of 80 eukaryotes. The variables are as follows:

Usage

data(eukaryotes_80)

Format

A data frame with 80 rows and 19 variables:

X.Organism.Name

Organism name at the species level

taxid

NCBI taxid

BioProject.Accession

BioProject Accession number (from BioProject database)

BioProject.ID

BioProject ID

Group

Commonly used organism groups: Animals, Fungi, Plants, Protists

SubGroup

NCBI Taxonomy level below group: Mammals, Birds, Fishes, Flatworms, Insects, Amphibians, Reptiles, Roundworms, Ascomycetes, Basidiomycetes, Land Plants, Green Algae, Apicomplexans, Kinetoplasts

Size..Mb.

Total length of DNA submitted for the project

GC.

Percent of nitrogenous bases (guanine or cytosine) in DNA submitted for the project

Assembly.Accession

Name of the genome assembly (from NCBI Assembly database)

Replicons

Number of replicons in the assembly

WGS

Four-letter Accession prefix followed by version as defined in WGS division of GenBank/INSDC

Scaffolds

Number of scaffolds in the assembly

Genes

Number of Genes annotated in the assembly

Proteins

Number of Proteins annotated in the assembly

Release.Date

First public sequence release for the project

Modify.Date

Sequence modification date for the project

Status

Highest level of assembly:
Chromosomes: one or more chromosomes are assembled
Scaffolds or contigs: sequence assembled but no chromosomes

Center

Origin of the sample

BioSample.Accession

BioSample Accession number

Genomic results

Description

A dataset containing information on Genome size and TE content for 808 taxids

Usage

data(gen_res)

Format

A data frame with 808 rows and 3 variables:

taxid

NCBI taxid

Genome_size

the Genome size in pb

TEcontent_bp

the transposable element content in pb

Reports whether x is a lifemap_obj object.

Description

Reports whether x is a lifemap_obj object.

Usage

is.lifemap_obj(x)

Arguments

x

The object to test.

Value

A boolean indicating whether or not the object is of lifemap_obj type.

Examples

## Only run examples in interactive R sessions
if (interactive()) {
data(LM_eukaryotes)
is.lifemap_obj(LM_eukaryotes)
}

Reports whether x is a lm_branches object.

Description

Reports whether x is a lm_branches object.

Usage

is.lm_branches(x)

Arguments

x

The object to test.

Value

A boolean indicating whether or not the object is of lm_branches type.

Reports whether x is a lm_markers object.

Description

Reports whether x is a lm_markers object.

Usage

is.lm_markers(x)

Arguments

x

The object to test.

Value

A boolean indicating whether or not the object is of lm_markers type.

Reports whether x is a lm_branches object.

Description

Reports whether x is a lm_branches object.

Usage

is.lm_piecharts(x)

Arguments

x

The object to test.

Value

A boolean indicating whether or not the object is of lm_piecharts type.

Kraken results

Description

A dataset containing NCBI information of 1000 eukaryotes. The variables are as follows:

Usage

data(kraken_res)

Format

A data frame with 4427 rows and 6 variables:

coverage_percent

Percentage of fragments covered by the clade rooted at this taxon

coverage_number

Number of fragments covered by the clade rooted at this taxon

fragment_number

Number of fragments assigned directly to this taxon

rank

A rank code, indicating (U)nclassified, (R)oot, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. Taxa that are not at any of these 10 ranks have a rank code that is formed by using the rank code of the closest ancestor rank with a number indicating the distance from that rank. E.g., "G2" is a rank code indicating a taxon is between genus and species and the grandparent taxon is at the genus rank.

taxid

NCBI taxonomic ID number

name

Indented scientific name

Initialise a new Lifemap visualisation.

Description

Initialise a lifemap_obj object. It can be used to describe aesthetics like the zoom level at which taxids becomes visible...

Usage

lifemap(lm_obj, zoom = 4)

Arguments

lm_obj

lifemap_obj object used for data visualisation.
zoom

The level of zoom for which values are displayed (if zoom = 0 only the nodes at the current zoom level or lower can have their values displayed).

Value

A lifemap_obj object.

Add a "branches" layer to a lifemap_obj object.

Description

Add a "branches" layer to a lifemap_obj object.

Usage

lm_branches(
  data = NULL,
  color = NULL,
  var_color = NULL,
  size = 5,
  min = 2,
  max = 20,
  opacity = 0.5,
  FUN = NULL,
  legend = TRUE,
  legendPosition = c("topright", "bottomright", "bottomleft", "topleft")
)

Arguments

data

A sub dataset to use, if NULL then all of the taxids from the lifemap object given to lifemap() will be used.
color

Either a color for the branches or a palette if a variable is used to represent branches' color.
var_color

A column name of the original dataframe to represent this variable by the color of branches.
size

Either a numeric for the branche's thickness or a variable to be represented by the branche's thickness.
min

An integer indicating the minimal thickness of the branches if the size is a column name.
max

An integer indicating the maximal thickness of the branches if the size is a column name.
opacity

An integer indicating branche's opacity.
FUN

The function to be applied to infer values. If NULL values won't be inferred
legend

A logical indicating whether or not to display the legend.
legendPosition

c("topright", "bottomright", "bottomleft", "topleft"), the position of the legend.

Value

An lm_branches object containing all aesthetics details for one layer of branches

Examples

data(LM_eukaryotes)

lm_branches(var_color = "GC.", color = "Accent")

lm_branches(data = LM_eukaryotes$df[LM_eukaryotes$df$Group %in% "Plants",])

Transformation in a LifemapR format of NCBI information for 1000 eukaryotes

Description

A dataset containing NCBI information of 1000 eukaryotes. The variables are as follows:

Usage

data(LM_eukaryotes)

Format

A lifemap object - a list containing the basemap used to fetch data and df, a data frame with 2760 rows and 26 variables:

X.Organism.Name

Organism name at the species level

taxid

NCBI taxid

BioProject.Accession

BioProject Accession number (from BioProject database)

BioProject.ID

BioProject ID

Group

Commonly used organism groups: Animals, Fungi, Plants, Protists

SubGroup

NCBI Taxonomy level below group: Mammals, Birds, Fishes, Flatworms, Insects, Amphibians, Reptiles, Roundworms, Ascomycetes, Basidiomycetes, Land Plants, Green Algae, Apicomplexans, Kinetoplasts

Size..Mb.

Total length of DNA submitted for the project

GC.

Percent of nitrogenous bases (guanine or cytosine) in DNA submitted for the project

Assembly.Accession

Name of the genome assembly (from NCBI Assembly database)

Replicons

Number of replicons in the assembly

WGS

Four-letter Accession prefix followed by version as defined in WGS division of GenBank/INSDC

Scaffolds

Number of scaffolds in the assembly

Genes

Number of Genes annotated in the assembly

Proteins

Number of Proteins annotated in the assembly

Release.Date

First public sequence release for the project

Modify.Date

Sequence modification date for the project

Status

Highest level of assembly:
Chromosomes: one or more chromosomes are assembled
Scaffolds or contigs: sequence assembled but no chromosomes

Center

Origin of the sample

BioSample.Accession

BioSample Accession number

lon

longitude of taxids on a specific basemap

lat

latitude of taxids on a specific basemap

sci_name

scientific name of taxids

zoom

zoom of taxids on a specific basemap

ascend

the list of all ancestors of taxids on a specific basemap

type

either "requested" if the taxid was given, "ancestor" if gotten from the database

ancestor

the direct ancestor oftaxids on a specific basemap

add a "markers" layer to a lifemap_obj object.

Description

Adds a layer with circles that can represent data. The main parameters that can be used to represent data are the following:

  • radius

  • var_fillColor

  • var_color (stroke's color)

Usage

lm_markers(
  data = NULL,
  radius = 10,
  min = 10,
  max = 40,
  fillColor = NULL,
  var_fillColor = NULL,
  fillOpacity = 0.8,
  stroke = FALSE,
  color = NULL,
  var_color = NULL,
  weight = 1,
  opacity = 0.8,
  legend = TRUE,
  legendPosition = c("topright", "bottomright", "bottomleft", "topleft"),
  legendOrientation = c("vertical", "horizontal"),
  legendOpacity = 0.5,
  FUN = NULL,
  display = c("auto", "requested", "all", "leaves"),
  popup = NULL,
  label = NULL
)

Arguments

data

A sub dataset to use, if NULL then all of the taxids from the lifemap object given to lifemap() will be used.
radius

Either a numerical value or a column name of the original dataframe to represent this variable by the size of markers.
min

An integer indicating the minimal size of the markers if radius is a column name.
max

An integer indicating the maximal size of the markers if radius is a column name.
fillColor

Either a color or a palette if the fillColor is represented by a variable.
var_fillColor

A column name of the original dataframe to represent this variable by the fillColor of markers.
fillOpacity

A numeric indicating the fill opacity.
stroke

A logical indicating whether to draw a border for markers.
color

The stroke color. Either a color or a palette if the stroke color is represented by a variable.
var_color

A column name of the original dataframe to represent this variable by the stroke color.
weight

The stroke width in pixels.
opacity

The stroke opacity.
legend

Whether to display the legend or not.
legendPosition

c("topright", "bottomright", "bottomleft", "topleft").
legendOrientation

c("vertical", "horizontal").
legendOpacity

Legend opacity (applies on the shapes in the legend, not the background itself).
FUN

The function to be applied to infer values. If NULL then the information missing from the parent nodes won't be inferred.
display

c("auto", "requested", "all", "leaves"), a string indicating how to display markers :

  • "auto" : the markers are displayed depending on the zoom level, by default, allow to have a lot of markers

  • "requested" : only displays the requested taxa, but all at the same time

  • "all" : displays all the taxa including all the ancestors to the root

  • "leaves" : displays only the latest (most recent) taxa

(WARNING : "requested", "leaves" and "auto" shouldn't be used to display more than 2000 markers as it may result in long computing time).
popup

A column name indicating what to display when clicking on a node.
label

A column name indicating what to display when hovering on a node.

Value

An lm_markers object containing all aesthetics details for one layer of markers.

Examples

data(LM_eukaryotes)

lm_markers(data = LM_eukaryotes$df[LM_eukaryotes$df$Group %in% "Plants", ])

lm_markers(radius = "GC.", var_fillColor = "Genes")

Add a "piecharts" layer to a lifemap_obj object.

Description

Add a "piecharts" layer to a lifemap_obj object.

Usage

lm_piecharts(
  data = NULL,
  param,
  type = c("pie", "bar", "polar-area", "polar-radius", "auto"),
  width = 30,
  height = 30,
  opacity = 1,
  showLabels = FALSE,
  pal = "Accent",
  legend = TRUE,
  legendPosition = c("topright", "bottomright", "bottomleft", "topleft"),
  display = c("auto", "requested", "all", "leaves")
)

Arguments

data

A sub dataset to use, if NULL then all of the taxids from the lifemap object given to lifemap() will be used.
param

A column name indicating the discret variable to be represented.
type

The type of chart to draw.
width

The maximal width of the charts.
height

The maximal height of the charts.
opacity

The chart's opacity.
showLabels

A boolean indicating whether to display the values directly on the chart or not.
pal

The palette to be used for the charts.
legend

A boolean indiacting whether to draw the legend or not.
legendPosition

c("topright", "bottomright", "bottomleft", "topleft"). Where should the legend be placed.
display

c("auto", "requested", "all", "leaves"), a string indicating how to display charts :

  • "auto" : the markers are displayed depending on the zoom level, by default, allow to have a lot of charts

  • "requested" : only displays the requested taxa, but all at the same time

  • "all" : displays all the taxa including all the ancestors to the root

  • "leaves" : displays only the latest (most recent) taxa

(WARNING : "requested", "leaves" and "auto" shouldn't be used to display more than 2000 charts as it may result in long computing time)

Value

An lm_piecharts object containing all aesthetics details for one layer of charts

Examples

data(LM_eukaryotes)

lm_piecharts(param = "Status")

lm_piecharts(data = LM_eukaryotes$df[LM_eukaryotes$df$Group %in% "Plants", ], param = "Status")

Create a newick for the given dataset.

Description

Create a newick for the given dataset.

Usage

make_newick(df)

Arguments

df

A dataframe either enriched with by the build_Lifemap function or containing at least two columns :

  • "taxid" containing NCBI format taxids

  • "ancestor" containing for each taxid, it's direct ancestor in the phylogeny

Value

A character string.

Infer numerical values to nodes.

Description

Infer numerical values to nodes.

Usage

pass_infos(M, FUN, value)

Arguments

M

The dataframe returned by create_matrix.
FUN

The function to be applied when inferring the values.
value

The column name to which the function applies.

Value

An array of values.

Examples

data(LM_eukaryotes)

infos <- create_matrix(LM_eukaryotes$df, c("GC.", "Genes"))

inferred_values <- pass_infos(M = infos, FUN = mean, value = "GC.")

Infer discret values to nodes for lm_piecharts function.

Description

Infer discret values to nodes for lm_piecharts function.

Usage

pass_infos_discret(M, value)

Arguments

M

The dataframe returned by create_matrix.
value

The column name represented as piecharts.

Value

A dataframe containing the TaxIDs and as many columns as there are distinct values.

Examples

data(LM_eukaryotes)

infos <- create_matrix(LM_eukaryotes$df, "Status")

inferred_values <- pass_infos_discret(M = infos, value = "Status")

Method to print lifemap_obj objects.

Description

Method to print lifemap_obj objects.

Usage

## S3 method for class 'lifemap_obj'
print(x, ...)

Arguments

x

An lifemap_obj.
...

Further arguments passed to or from other methods.

Value

Either a description of the dataframe and basemap used for the lm_obj object, or a shiny application if aesthetics are furnished

Examples

## Only run examples in interactive R sessions
if (interactive()) {
data(LM_eukaryotes)
print(LM_eukaryotes)
}