plotMap: Plotting of maps
In R.SamBada: Processing Pipeline for 'SamBada' from Pre- To Post-Processing

Description Usage Arguments Value Author(s) Examples

Plots several kinds of maps (environmental variable distribution, population structure, marker absence or presence, autocorrelation of marker). Unlike plotResultInteractive, the resulting maps are non-interactive. The function can handle several marker/variables at once and create separate output files.

plotMap(
  envFile,
  x,
  y,
  locationProj,
  popStrCol,
  gdsFile,
  markerName,
  mapType,
  varEnvName,
  SAMethod = NULL,
  SAThreshold = NULL,
  saveType = NULL,
  rasterName = NULL,
  simultaneous = FALSE
)

`envFile`	char The file containing the input environmental variable of sambada.
`x`	char The name of the column corresponding to the x-coordinate in the `envFile`. Can be set to null if unknown, in this case the maps will not be available
`y`	char The name of the column corresponding to the y-coordinate in the env file. Can be set to null if x is null.
`locationProj`	integer EPSG code of the geographical projection in the `envFile`
`popStrCol`	char The name or vector of name of column(s) in `envFile` describing population structure. If provided, additional layers on the map will be available representing population structure.
`gdsFile`	char The GDS file created in the preprocessing of sambada. If null, will try with `envFile`(without -env.csv) and .gds
`markerName`	name of the marker to be plotter if `mapType` is 'marker' or 'AS'. `markerName` can be found in preparedOutput$sambadaOutput[,”] where preparedOutput would be the result of the function `prepareOutput`
`mapType`	char A string or vector of string containing one or several of 'marker' (presence/absence of marker), 'env' (environmental variable distribution), 'popStr' (population variable on continuous scale), 'popPieChart' (belonging to a population in pie charts), 'AS' (autocorrelation of the marker). Note that the background of all maps, if found, will be the raster of the environmental variable. Thus the 'env' `mapType` is preferred when no raster is provided. For the 'AS' type, it is calculated on the fly for the markers provided and not the one possibly calculated by sambada.
`varEnvName`	char Name of the environmental variable. If a raster of the variable is located in your working directory, you can provide `varEnvName` even for `mapType` such as 'marker' or 'AS'. The function will scan the folder of your working directory for raster with the same name as `varEnvName` (and commonly used extension for raster) and put it as background.
`SAMethod`	char If `mapType` contains 'AS', then you must specify the method for setting the weights of neighbours. Can be one of 'knn' (k-nearest neighbours) or 'distance'
`SAThreshold`	char If `mapType` contains 'AS' and `SAMethod` is 'knn' then the number of neighbours. If `SAMethod` is 'distance' then the distance in map-unit (unless you use a spherical projection (latitude/longitude), in which case you should use km)
`saveType`	char One of NULL, 'png' or 'pdf'. If NULL is set, the maps will be shown in the R plotting window. Otherwise, it will be saved in the specified format in your working directory.
`rasterName`	char If a raster file with the environmental variable distribution exists with a different name than `varEnvName`, provide it here (including extension)
`simultaneous`	boolean If TRUE and `mapType` contains several kinds of maps, all maps corresponding to the same marker will be plotted on the same window. The resulting maps can be very small.

None

Solange Duruz

# Define right GDS file according to your OS
if(Sys.info()['sysname']=='Windows'){
  gdsFile=system.file("extdata", "uganda-subset-mol_windows.gds", package = "R.SamBada")
} else {
  gdsFile=system.file("extdata", "uganda-subset-mol_unix.gds", package = "R.SamBada")
}
#############
# Run plotMap
#############
# Map of environmental variable

plotMap(envFile=system.file("extdata", "uganda-subset-env-export.csv", package = "R.SamBada"), 
     x='longitude', y='latitude', locationProj=4326,  popStrCol='pop1', gdsFile=gdsFile, 
     markerName='Hapmap28985-BTA-73836_GG', mapType='env', varEnvName='bio1', 
     simultaneous=FALSE)

plotMap(envFile=system.file("extdata", "uganda-subset-env-export.csv", package = "R.SamBada"), 
     x='longitude', y='latitude', locationProj=4326,  popStrCol='pop1', gdsFile=gdsFile, 
     markerName='Hapmap28985-BTA-73836_GG', mapType='marker', varEnvName='bio1', 
     simultaneous=FALSE)

# Maps of marker and population structure (two subplot)
plotMap(envFile=system.file("extdata", "uganda-subset-env-export.csv", package = "R.SamBada"),
     'longitude','latitude', locationProj=4326,  popStrCol='pop1', 
     gdsFile=gdsFile, markerName='Hapmap28985-BTA-73836_GG', 
     mapType=c('marker', 'popStr'), varEnvName='bio1', simultaneous=TRUE)