View source: R/vis_geography.R
hapDistribution | R Documentation |
show distribution of intereted haplotypes on maps
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,
...
)
hap |
an object of hapResult class |
AccINFO |
a data.frame contains accession information |
LON.col , LAT.col |
column names of
longitude( |
hapNames |
haplotype names used for display |
database |
character string naming a geographical database, a list of
|
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 |
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 |
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 |
No return value
data("geneHapR_test")
hapDistribution(hapResult,
AccINFO = AccINFO,
LON.col = "longitude",
LAT.col = "latitude",
hapNames = c("H001", "H002", "H003"))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.