[adegenet-forum] help with sPCA basics: plotting a raster map with xy points overlaid

[Caroline Judy]

Dear Adegenet forum,

As a first step to the sPCA, I am trying to plot the xy points on the topo
map using the following code similar to the example "rupica" in the SPCA
tutorial that appears on page 27.

plot(data$other$topo.jam)

points(xy,col="red", pch=20)
Both the xy points and the map of my study region are part of the Genind
object I created, see details below.



---------------

/// GENIND OBJECT /////////

 // 158 individuals; 6,451 loci; 12,902 alleles; size: 10.7 Mb

 // Basic content
   @tab:  158 x 12902 matrix of allele counts
   @loc.n.all: number of alleles per locus (range: 2-2)
   @loc.fac: locus factor for the 12902 columns of @tab
   @all.names: list of allele names for each locus
   @ploidy: ploidy of each individual  (range: 2-2)
   @type:  codom
   @call: read.structure(file =
"~/Documents/Trochilus/second_chapter/Analysis/structure/input/GBS_all_pop_pheno.stru",
    n.ind = 158, n.loc = 6451, onerowperind = TRUE, col.lab = 1,
    col.pop = 2, col.others = 3:8, row.marknames = 0, ask = FALSE)

 // Optional content
   @pop: population of each individual (group size range: 6-37)
   @strata: a data frame with 3 columns ( sex, phenotype, HI )
   @other: a list containing: X  xy  topo  topo.east  topo.jam
--------------------------------------------------------------------------------------
$topo.jam
class       : RasterLayer
band        : 1  (of  3  bands)
dimensions  : 1416, 2558, 3622128  (nrow, ncol, ncell)
resolution  : 0.0008333333, 0.0008333333  (x, y)
extent      : -78.27649, -76.14482, 17.48716, 18.66716  (xmin, xmax, ymin,
ymax)
coord. ref. : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84
+towgs84=0,0,0
data source :
/Users/carolineduffie/Documents/Trochilus/second_chapter/Analysis/PCA/sPCA/jamaica_elevation.tif
names       : jamaica_elevation
values      : 0, 255  (min, max)
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