# Load packagelibrary(mapmixture)# Read in admixture file format 1file<- system.file("extdata","admixture1.csv",package="mapmixture")admixture1<- read.csv(file)# Read in coordinates filefile<- system.file("extdata","coordinates.csv",package="mapmixture")coordinates<- read.csv(file)# Run mapmixturemap1<- mapmixture(admixture1,coordinates,crs=3035)# map1

# Load packageslibrary(mapmixture)library(rnaturalearthhires)# Install rnaturalearthhires package using:# install.packages("rnaturalearthhires", repos = "https://ropensci.r-universe.dev", type = "source")# Read in admixture file format 1file<- system.file("extdata","admixture1.csv",package="mapmixture")admixture1<- read.csv(file)# Read in coordinates filefile<- system.file("extdata","coordinates.csv",package="mapmixture")coordinates<- read.csv(file)# Run mapmixturemap2<- mapmixture(admixture_df=admixture1,coords_df=coordinates,cluster_cols= c("#f1a340","#998ec3"),cluster_names= c("Group A","Group B"),crs=3035,basemap=rnaturalearthhires::countries10[, c("geometry")],boundary= c(xmin=-15,xmax=16,ymin=40,ymax=62),pie_size=1,pie_border=0.3,pie_border_col="white",pie_opacity=1,land_colour="#d9d9d9",sea_colour="#deebf7",expand=TRUE,arrow=TRUE,arrow_size=1.5,arrow_position="bl",scalebar=TRUE,scalebar_size=1.5,scalebar_position="tl",plot_title="Admixture Map",plot_title_size=12,axis_title_size=10,axis_text_size=8)# map2

# Load packagelibrary(mapmixture)# Read in admixture file format 3file<- system.file("extdata","admixture3.csv",package="mapmixture")admixture3<- read.csv(file)# Read in coordinates filefile<- system.file("extdata","coordinates.csv",package="mapmixture")coordinates<- read.csv(file)# Run mapmixturemap3<- mapmixture(admixture3,coordinates,crs=3035)# map3

# Load packageslibrary(mapmixture)library(ggplot2)# Read in admixture file format 1file<- system.file("extdata","admixture1.csv",package="mapmixture")admixture1<- read.csv(file)# Read in coordinates filefile<- system.file("extdata","coordinates.csv",package="mapmixture")coordinates<- read.csv(file)# Run mapmixturemap4<- mapmixture(admixture_df=admixture1,coords_df=coordinates,cluster_cols= c("#f1a340","#998ec3"),cluster_names= c("Ancestry 1","Ancestry 2"),crs=4326,boundary= c(xmin=-15,xmax=16,ymin=40,ymax=62),pie_size=1,)+# Add additional label to the map  annotate("label",x=-10,y=46.5,label="Atlantic Ocean",size=3,  )+# Add additional text to the map  annotate("text",x=2.5,y=57,label="North Sea",size=3,  )+# Adjust ggplot theme options  theme(axis.title= element_text(size=10),axis.text= element_text(size=8),  )+# Adjust the size of the legend keys  guides(fill= guide_legend(override.aes=list(size=5,alpha=1)))# map4

# Load packageslibrary(mapmixture)library(ggplot2)library(gridExtra)# Read in admixture file format 1file<- system.file("extdata","admixture1.csv",package="mapmixture")admixture1<- read.csv(file)# Read in coordinates filefile<- system.file("extdata","coordinates.csv",package="mapmixture")coordinates<- read.csv(file)# Run mapmixturemap5<- mapmixture(admixture_df=admixture1,coords_df=coordinates,cluster_cols= c("#f1a340","#998ec3"),cluster_names= c("Ancestry 1","Ancestry 2"),crs=4326,boundary= c(xmin=-20,xmax=20,ymin=40,ymax=62),pie_size=1.3,)+# Adjust theme options  theme(legend.position="top",plot.margin= margin(l=10,r=10),  )+# Adjust the size of the legend keys  guides(fill= guide_legend(override.aes=list(size=5,alpha=1)))# Traditional structure barplotstructure_barplot<- structure_plot(admixture_df=admixture1,type="structure",cluster_cols= c("#f1a340","#998ec3"),site_dividers=TRUE,divider_width=0.4,site_order= c("Vigo","Ile de Re","Isles of Scilly","Mullet Peninsula","Shetland","Cromer","Helgoland","Flodevigen","Lysekil","Bergen"  ),labels="site",flip_axis=FALSE,site_ticks_size=-0.05,site_labels_y=-0.35,site_labels_size=2.2)+# Adjust theme options  theme(axis.title.y= element_text(size=8,hjust=1),axis.text.y= element_text(size=5),  )# Arrange plots# grid.arrange(map5, structure_barplot, nrow = 2, heights = c(4,1))

# Load packageslibrary(mapmixture)library(ggplot2)library(gridExtra)# Read in admixture file format 1file<- system.file("extdata","admixture1.csv",package="mapmixture")admixture1<- read.csv(file)# Read in coordinates filefile<- system.file("extdata","coordinates.csv",package="mapmixture")coordinates<- read.csv(file)# Run mapmixturemap6<- mapmixture(admixture_df=admixture1,coords_df=coordinates,cluster_cols= c("#f1a340","#998ec3"),cluster_names= c("Ancestry 1","Ancestry 2"),crs=4326,boundary= c(xmin=-20,xmax=20,ymin=40,ymax=62),pie_size=1.3,)+# Adjust theme options  theme(legend.position="top",plot.margin= margin(l=10,r=10),  )+# Adjust the size of the legend keys  guides(fill= guide_legend(override.aes=list(size=5,alpha=1)))# Facet structure barplotfacet_barplot<- structure_plot(admixture1,type="facet",cluster_cols= c("#f1a340","#998ec3"),facet_col=2,ylabel="Admixture proportions",)+  theme(axis.title.y= element_text(size=10),axis.text.y= element_text(size=5),strip.text= element_text(size=6,vjust=1,margin= margin(t=1.5,r=0,b=1.5,l=0)),  )# Arrange plots# grid.arrange(map6, facet_barplot, ncol = 2, widths = c(3,2))

# Load packageslibrary(mapmixture)library(terra)# Create SpatRaster objectearth<-terra::rast("../NE1_50M_SR_W/NE1_50M_SR_W.tif")# Read in admixture file format 1file<- system.file("extdata","admixture1.csv",package="mapmixture")admixture1<- read.csv(file)# Read in coordinates filefile<- system.file("extdata","coordinates.csv",package="mapmixture")coordinates<- read.csv(file)# Run mapmixturemap7<- mapmixture(admixture1,coordinates,crs=3035,basemap=earth)# map7

# Load packageslibrary(mapmixture)library(rnaturalearthhires)library(ggplot2)library(dplyr)library(sf)# Read in admixture file format 1file<- system.file("extdata","admixture1.csv",package="mapmixture")admixture1<- read.csv(file)# Read in coordinates filefile<- system.file("extdata","coordinates.csv",package="mapmixture")coordinates<- read.csv(file)# Parameterscrs<-3035boundary<- c(xmin=-11,xmax=13,ymin=50,ymax=60)|> transform_bbox(bbox= _,crs)# Read in world countries from Natural Earth and transform to CRSworld<-rnaturalearthhires::countries10[, c("geometry")]world<- st_transform(world,crs=crs)# Read in Marine Conservation Zones shapefile# Extract polygons for Western Channel, Offshore Brighton and Swallow Sand# Transform to CRSmczs<- st_read("../Marine_Conservation_Zones_England/Marine_Conservation_Zones___Natural_England_and_JNCC.shp",quiet=TRUE)|>dplyr::filter(.data= _,MCZ_NAME%in% c("Western Channel","Offshore Brighton","Swallow Sand"))|>  st_transform(x= _,crs=crs)# Run mapmixture helper functions to prepare admixture and coordinates dataadmixture_df<- standardise_data(admixture1,type="admixture")|> transform_admix_data(data= _)coords_df<- standardise_data(coordinates,type="coordinates")admix_coords<- merge_coords_data(coords_df,admixture_df)|> transform_df_coords(df= _,crs=crs)# Plot map and add pie chartsmap8<- ggplot()+  geom_sf(data=world,colour="black",fill="#d9d9d9",size=0.1)+  geom_sf(data=mczs, aes(fill="MCZs"),linewidth=0.3)+  scale_fill_manual(values= c("yellow"))+  coord_sf(xlim= c(boundary[["xmin"]],boundary[["xmax"]]),ylim= c(boundary[["ymin"]],boundary[["ymax"]])  )+  add_pie_charts(admix_coords,admix_columns=4:ncol(admix_coords),lat_column="lat",lon_column="lon",pie_colours= c("green","blue"),border=0.3,opacity=1,pie_size=0.8  )+  theme(legend.title= element_blank(),  )# map8

# Load packageslibrary(mapmixture)library(ggplot2)library(adegenet)library(RColorBrewer)library(gridExtra)# Load example genotypesdata("dapcIllus")geno=dapcIllus$a# Change population labelspopNames(geno)= c("Pop1","Pop2","Pop3","Pop4","Pop5","Pop6")# Region namesregion_names<- rep(c("Region1","Region2"),each=300)# Define colour palettecols= brewer.pal(nPop(geno),"RdYlBu")# Perform PCApca1= dudi.pca(geno,scannf=FALSE,nf=3)# Percent of genetic variance explained by each axispercent= round(pca1$eig/sum(pca1$eig)*100,digits=1)# Scatter plot with centroids and segmentsscatter1<- scatter_plot(dataframe=pca1$li,group_ids=geno$pop,type="points",axes= c(1,2),percent=percent,colours=cols,point_size=2,point_type=21,centroid_size=2,stroke=0.1,plot_title="PCA coloured by group_ids")+  theme(legend.position="none",axis.title= element_text(size=8),axis.text= element_text(size=6),plot.title= element_text(size=10),  )# Same as scatter1 but no segments and axis 1 and 3 are shownscatter2<- scatter_plot(dataframe=pca1$li,group_ids=geno$pop,type="points",axes= c(1,3),percent=percent,colours=cols,point_size=2,point_type=21,centroids=TRUE,centroid_size=2,segments=FALSE,stroke=0.1,plot_title="PCA no segments and axis 1 and 3 shown")+  theme(legend.position="none",axis.title= element_text(size=8),axis.text= element_text(size=6),plot.title= element_text(size=10),  )# Same as scatter1 but coloured by regionscatter3<- scatter_plot(dataframe=pca1$li,group_ids=geno$pop,other_group=region_names,type="points",axes= c(1,2),percent=percent,colours=cols,point_size=2,point_type=21,centroid_size=2,stroke=0.1,plot_title="PCA coloured by other_group")+  theme(legend.position="none",axis.title= element_text(size=8),axis.text= element_text(size=6),plot.title= element_text(size=10),  )# Scatter plot with labels instead of pointsscatter4<- scatter_plot(dataframe=pca1$li,group_ids=geno$pop,type="labels",labels= rownames(pca1$li),colours=cols,size=2,label.size=0.10,label.padding= unit(0.10,"lines"),plot_title="PCA using labels instead of points")+  theme(legend.position="none",axis.title= element_text(size=8),axis.text= element_text(size=6),plot.title= element_text(size=10),  )# Arrange plots# grid.arrange(scatter1, scatter2, scatter3, scatter4)