Differentiation
and
Heterozygosity
D.bar
object.Ancestry_barchart
ind.order
and pop.order
arguments,
respectively.legend_pos
argument.The following updates laregly apply for the
Plot_coordinates
, Piechart_map
,
Point_map
, and Network_map
functions. We note
where any updates are function specific.
country_code
argument. Country codes must match those used
in geodata.group
argument and group_col
argument to specify colors for each
group (only for Plot_coordinates
).legend_pos
argument.scale_bar
and north_arrow
arguments. Users can
also modify the position and style of the north arrow using
north_arrow_position
and north_arrow_style
arguments, respectively.shapefile
argument. Users can also control where the shapefile is placed using
shape_file_position
, the fill color
(shapefile_col
), and the outline color
(shapefile_outline_col
). Shapefiles can be character
strings or spatVector objects.raster
, raster_col
, and
raster_plot_position
arguments. Custom breaks can be set
with raster_breaks
and users can indicate if rasters are
discrete using discrete_raster
. Note that sometimes
terra
interprets continuous rasters as discrete, and users
should use the discrete_raster
argument to accommodate
this. Rasters can be characters or spatRaster objects.Pairwise_heatmap
Differentiation
function
has been updated to be consistent with the rest of the function (using
!is.na).Dif_stats
,
Dif_stats_map
, Div_stats
,
Div_stats_map
, and Plot_Ancestry
functions
have been removed.Longitude_col
and Latitude_col
arguments have been added to mapping functions;
Plot_coordinates
, Ancestry_Piemap
,
Piechart_map
, Network_map
, and
Point_map
.Ind_order
and Pop_order
arguments have
been added to Ancestry_Barchart
to allow users to specify
the order of individuals and populations in the barchart.Plot_coordinates
function has been added to make
sample maps from coordinates.Point_map
function has replaced
Div_stats_map
and a statistic argument has been added to
highlight the functions utility and allow users to name the map
legend.Dif_stats_map
has been changed to
Network_map
and a statistic argument has been added to
highlight the functions utility and allow users to name the map
legend.Plot_ancestry
has been split into
Piechart_Map
and Ancestry_barchart
so that it
is easier for users to determine which function is most appropriate for
their analysis.Differentiation
has been added to estimate Fst, Nei’s
D, and Jost’s D. Please see the documentation for more details.Heterozygosity
has been added to estimate 7 different
measures of heterozygosity. Please see the documentation for more
details.Private.alleles
has been added to calculate the number
of private alleles in each population.Dif_Stats
function has been deprecated, please used
the Differentiation
function to calculate pairwise
differentiation between populations (Fst, Nei’s D, Jost’s D) or
individuals (Nei’s D).Div_Stats
function has been deprecated, please use
the Heterozygosity
function if you wish to estimate
heterozygosity or the Private.alleles
function if you wish
to calculate the number of private alleles per population. Please use
the Point_Map
function if you wish to visualize the results
on a map or plot.Dif_stats_Map
, Div_Stats_Map
, and
Plot_ancestry
have been updated to use a base color of
#f4f4f4 instead of grey99 which was throwing an error for some
users.Plot_ancestry
,
the original value of 0.35 was found to be too high, especially in cases
where users were mapping a smaller geographic area.Div_Stats
and Dif_stats
have been updated
to accept a vcf file or vcfR object as input.Div_Stats
and Dif_stats
have been updated
to accept a csv file or data frame for population assignment.Plot_ancestry
has been updated to generate
structure-like plots using ggplot2 instead of base R and to handle
character and numeric values for individual and population names. Note
that individual and populations must be of the same type (i.e., both
numeric or both characters).rnaturalearth
is no longer used. We now
use spData
for mapping data.Div_Stats
and
Dif_stats
so that files are not automatically written to
the working directory.