| Title: | Data Visualisation on 'Lifemap' Tree |
| Version: | 1.1.5 |
| Imports: | leaflet, shiny, jsonlite, dplyr, tidyr, leaflet.minicharts, htmltools, rlang, RCurl, fastmatch, arrow |
| Description: | Allow to visualise data on the NCBI phylogenetic tree as presented in Lifemap https://lifemap.cnrs.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. |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.2 |
| Depends: | R (≥ 4.1.0) |
| Suggests: | knitr |
| VignetteBuilder: | knitr |
| URL: | https://lifemap-tol.github.io/LifemapR/, https://github.com/Lifemap-ToL/LifemapR |
| BugReports: | https://github.com/Lifemap-ToL/LifemapR/issues |
| NeedsCompilation: | no |
| Packaged: | 2025-03-06 08:16:02 UTC; siberchicot |
| Author: | Cassandra Bompard [aut],
Damien M. de Vienne
 [aut],
Julien Barnier
[aut],
Aurélie Siberchicot
[ctb, cre] |
| Maintainer: | Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> |
| Repository: | CRAN |
| Date/Publication: | 2025-03-06 10:40:12 UTC |
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()
}
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
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 = NULL, 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 |
Deprecated argument. |
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)
## 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 = NULL)
Arguments
df |
A dataframe. If given, its columns can be easily accessed with "~" (eg. ~GC.). |
basemap |
Deprecated argument. |
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",])
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 :
(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 :
(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$Group %in% "Plants", ], param = "Status")
Create a newick for the given dataset.
Description
Create a newick for the given dataset.
Usage
make_newick(df)
Arguments
df |
A dataframe either enriched with by the build_Lifemap function or containing at least two columns :
|
Value
A character string.
Infer numerical values to nodes.
Description
Infer numerical values to nodes.
Usage
pass_infos(M, FUN, value)
Arguments
M |
The dataframe returned by create_matrix. |
FUN |
The function to be applied when inferring the values. |
value |
The column name to which the function applies. |
Value
An array of values.
Examples
data(LM_eukaryotes)
infos <- create_matrix(LM_eukaryotes$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)
}