hapDistribution {geneHapR}

Display of Geography Distribution

Description

show distribution of intereted haplotypes on maps

Usage

hapDistribution(
  hap,
  AccINFO,
  LON.col,
  LAT.col,
  hapNames,
  database = "world",
  regions = ".",
  hap.color = hap.color,
  zColours = zColours,
  legend = TRUE,
  symbolSize = 1,
  symbol.lim = c(1, 10),
  ratio = 1,
  cex.legend = 0.8,
  lwd.pie = 1,
  borderCol.pie = NA,
  lty.pie = 1,
  showlabel = TRUE,
  label.col = "black",
  label.cex = 0.8,
  label.font = 1,
  label.adj = c(0.5, 0.5),
  map.fill.color = 1,
  ...
)

Arguments

hap

an object of hapResult class

AccINFO

a data.frame contains accession information

LON.col, LAT.col

column names of longitude(LON.col) and latitude(LAT.col)

hapNames

haplotype names used for display

database

character string naming a geographical database, a list of x, y, and names obtained from a previous call to map or a spatial object of class SpatialPolygons or SpatialLines. The string choices include a world map, three USA databases (usa, state, county), and more (type help(package='maps') to see the package index). If the requied database is in a different package that has not been attached, the string may be started with "packagename::". The location of the map databases may be overridden by setting the R_MAP_DATA_DIR environment variable.

regions

character vector that names the polygons to draw. Each database is composed of a collection of polygons, and each polygon has a unique name. When a region is composed of more than one polygon, the individual polygons have the name of the region, followed by a colon and a qualifier, as in michigan:north and michigan:south. Each element of regions is matched against the polygon names in the database and, according to exact, a subset is selected for drawing. The regions may also be defined using (perl) regular expressions. This makes it possible to use 'negative' expressions like "Norway(?!:Svalbard)", which means Norway and all islands except Svalbard. All entries are case insensitive. The default selects all polygons in the database.

hap.color, zColours

colors to apply to the pie section for each attribute column, "zColours" will be detached in future.

legend

a keyword specified the position of legend, one of "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" and "center"; or a numeric vector of length two contains x,y coordinate of the legend

symbolSize

a numeric specified the symbol size. It will be detached in future. Please use "symbol.lim" instead.

symbol.lim

a numeric vector give the maximum and minimum size of each symbol

ratio

the ratio of Y to N in the output map, set to 1 as default

cex.legend

character expansion factor for legend relative to current par("cex")

lwd.pie

line width of the pies

borderCol.pie

The color of pie's border, default is NA, which means no border will be plotted

lty.pie

the line type of pie border

showlabel

a bool vector indicates whether show the labels which represens number of individuals. Default as TRUE.

label.col

color of the labels, default as "black"

label.cex

a number indicates the text size in label, default as 0.8

label.font

Font of label, 1 for normal, 2 for bold, 3 for italica, 4 for bold-italica

label.adj

the position of label, default as c(0.5, 0.5)

map.fill.color

vector of colors. If fill is FALSE, the first color is used for plotting all lines, and any other colors are ignored. Otherwise, the colors are matched one-one with the polygons that get selected by the region argument (and are reused cyclically, if necessary). If fill = TRUE, the default boundary line colour is given by par("fg"). To change this, you can use the border argument (see '...'). A color of NA causes the corresponding region to be deleted from the list of polygons to be drawn. Polygon colors are assigned after polygons are deleted due to values of the xlim and ylim arguments

...

Extra arguments passed to polygon or lines. Of particular interest may be the options border andlty that control the color and line type of the polygon borders when fill = TRUE.

Value

No return value

Examples

data("geneHapR_test")
hapDistribution(hapResult,
                AccINFO = AccINFO,
                LON.col = "longitude",
                LAT.col = "latitude",
                hapNames = c("H001", "H002", "H003"))