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add a "markers" layer to a lifemap_obj object.

Source: R/lm_markers.R
lm_markers.Rd

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", ])
#> $taxids
#> [[1]]
#>  [1] "2711"    "3055"    "3077"    "3088"    "3352"    "3435"    "3555"   
#>  [8] "3635"    "3641"    "3668"    "3702"    "3708"    "3710"    "3712"   
#> [15] "3726"    "3760"    "3823"    "3847"    "3871"    "3880"    "3888"   
#> [22] "3915"    "4002"    "4072"    "4083"    "4097"    "4113"    "4513"   
#> [29] "4516"    "4529"    "4530"    "4577"    "4679"    "13288"   "13419"  
#> [36] "29656"   "34315"   "34316"   "38846"   "39905"   "39919"   "39946"  
#> [43] "39955"   "44586"   "49829"   "53169"   "55890"   "57919"   "59691"  
#> [50] "69181"   "80294"   "80754"   "83906"   "85692"   "96569"   "102169" 
#> [57] "109997"  "110450"  "112509"  "122812"  "123599"  "126366"  "128810" 
#> [64] "130453"  "157748"  "160369"  "176864"  "178133"  "210143"  "228173" 
#> [71] "296587"  "310722"  "314410"  "357465"  "462830"  "586396"  "586722" 
#> [78] "1000413" "1010633" "1042139" "1381980" "1711249" "1862640" "1985974"
#> [85] "2303040" "2589997" "2758712" "2905994"
#> 
#> 
#> $radius
#> [1] "default"
#> 
#> $value
#> [1] 10
#> 
#> $fillColor
#> [1] "red"
#> 
#> $fillPalette
#> NULL
#> 
#> $min
#> [1] 10
#> 
#> $max
#> [1] 40
#> 
#> $FUN
#> NULL
#> 
#> $stroke
#> [1] FALSE
#> 
#> $color
#> [1] "black"
#> 
#> $palette
#> NULL
#> 
#> $weight
#> [1] 1
#> 
#> $opacity
#> [1] 0.8
#> 
#> $fillOpacity
#> [1] 0.8
#> 
#> $var_fillColor
#> [1] "default"
#> 
#> $var_color
#> [1] "default"
#> 
#> $legend
#> [1] TRUE
#> 
#> $legendPosition
#> [1] "topright"
#> 
#> $legendOrientation
#> [1] "vertical"
#> 
#> $legendOpacity
#> [1] 0.5
#> 
#> $display
#> [1] "auto"
#> 
#> $popup
#> NULL
#> 
#> $label
#> NULL
#> 

lm_markers(radius = "GC.", var_fillColor = "Genes")
#> $taxids
#> NULL
#> 
#> $radius
#> [1] "GC."
#> 
#> $value
#> NULL
#> 
#> $fillColor
#> NULL
#> 
#> $fillPalette
#> [1] "RdBu"
#> 
#> $min
#> [1] 10
#> 
#> $max
#> [1] 40
#> 
#> $FUN
#> NULL
#> 
#> $stroke
#> [1] FALSE
#> 
#> $color
#> [1] "black"
#> 
#> $palette
#> NULL
#> 
#> $weight
#> [1] 1
#> 
#> $opacity
#> [1] 0.8
#> 
#> $fillOpacity
#> [1] 0.8
#> 
#> $var_fillColor
#> [1] "Genes"
#> 
#> $var_color
#> [1] "default"
#> 
#> $legend
#> [1] TRUE
#> 
#> $legendPosition
#> [1] "topright"
#> 
#> $legendOrientation
#> [1] "vertical"
#> 
#> $legendOpacity
#> [1] 0.5
#> 
#> $display
#> [1] "auto"
#> 
#> $popup
#> NULL
#> 
#> $label
#> NULL
#>