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app.R
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#Startup----
library(shiny)
library(shinyWidgets)
library(leaflet)
library(ggplot2)
library(dplyr)
library(purrr)
library(tidyr)
library(sf)
library(sp)
library(RPostgreSQL)
library(ggdendro)
library(hrbrthemes)
library(FactoMineR)
library(factoextra)
library(ggnewscale)
#Attributes----
{
heightLegend <- 100
options(scipen = 999)
contx <- scale_x_continuous()
logx <- scale_x_log10()
variab <- c("Cultures" = "culture_id",
"Regions" = "region_id",
"Typological Groups" = "find_character_id",
"Cluster" = "mclust",
"Cluster Group" = "mclust_group",
"Periods" = "zt_id",
"Period-Groups" = "zt_group_id")
con <- dbConnect(drv = dbDriver("PostgreSQL"),
host = "archmetal.nerdnose.net",
dbname = "postgres",
user = "postgres",
password = "Postgresfo24")
culture.import <- dbGetQuery(con, "
select culture_id, culture_en, culture_dt, color, shape
from cau.culture join cau.feature using (culture_id) join cau.site using (site_id)
where region_id=1 or region_id = 2 or region_id = 3 or region_id = 4 or region_id = 5 or region_id = 6 or region_id = 17 or region_id = 18 or region_id = 19 or region_id = 20 or region_id = 21
group by culture_id, culture_en, culture_dt, color, shape
order by culture_en
")
culture_id <- list(
setNames(culture.import$color, culture.import$culture_id),
setNames(culture.import$culture_en, culture.import$culture_id),
setNames(culture.import$culture_dt, culture.import$culture_id),
setNames(culture.import$shape, culture.import$culture_id))
names(culture_id) <- c("col", "en", "dt", "shape")
find_character.import <- dbGetQuery(con, "select * from cau.find_character")
find_character_id <- list(
setNames(find_character.import$color, find_character.import$find_character_id),
setNames(find_character.import$find_character_en, find_character.import$find_character_id),
setNames(find_character.import$find_character_dt, find_character.import$find_character_id),
setNames(find_character.import$shape, find_character.import$find_character_id))
names(find_character_id) <- c("col", "en", "dt", "shape")
region.import <- dbGetQuery(con, "select * from cau.region
where region_id=1 or region_id = 2 or region_id = 3 or region_id = 4 or region_id = 5 or region_id = 6 or region_id = 17 or region_id = 18 or region_id = 19 or region_id = 20 or region_id = 21 or region_id = 22 or region_id = 23 or region_id = 24 or region_id = 26
")
region_id <- list(
setNames(region.import$color, region.import$region_id),
setNames(region.import$region_en, region.import$region_id),
setNames(region.import$region_dt, region.import$region_id),
setNames(region.import$shape, region.import$region_id))
names(region_id) <- c("col", "en", "dt", "shape")
site.import <- dbGetQuery(con, "select site_id, site_dt from cau.site
where region_id=1 or region_id = 2 or region_id = 3 or region_id = 4 or region_id = 5 or region_id = 6 or region_id = 17 or region_id = 18 or region_id = 19 or region_id = 20 or region_id = 21 or region_id = 22 or region_id = 23 or region_id = 24 or region_id = 26
")
site_id <- list(
setNames(site.import$site_dt, site.import$site_id),
setNames(site.import$site_dt, site.import$site_id))
names(site_id) <- c("en", "dt")
zt.import <- dbGetQuery(con,
"
select zt_id, zt_en, zt_dt, min, max, color, shape
from cau.zt join cau.feature using (zt_id) join cau.site using (site_id) join cau.find using (feature_id, site_id)
where region_id=1 or region_id = 2 or region_id = 3 or region_id = 4 or region_id = 5 or region_id = 6 or region_id = 17 or region_id = 18 or region_id = 19 or region_id = 20 or region_id = 21 or region_id = 22 or region_id = 23 or region_id = 24 or region_id = 26
group by zt_id, zt_en, zt_dt, min, max, color, shape
order by min, max
")
zt.import$choice_en <- paste0(zt.import$zt_en, "(", zt.import$min, "-", zt.import$max, ")")
zt.import$choice_dt <- paste0(zt.import$zt_dt, "(", zt.import$min, "-", zt.import$max, ")")
zt_id <- list(
setNames(zt.import$color, zt.import$zt_id),
setNames(zt.import$shape, zt.import$zt_id),
setNames(zt.import$choice_en, zt.import$zt_id),
setNames(zt.import$choice_dt, zt.import$zt_id))
names(zt_id) <- c("col", "shape", "en", "dt")
zt_group.import <- dbGetQuery(con, "select * from cau.zt_group;")
zt_group_id <- list(
setNames(zt_group.import$color, zt_group.import$zt_group_id),
setNames(zt_group.import$zt_group_en, zt_group.import$zt_group_id),
setNames(zt_group.import$zt_group_dt, zt_group.import$zt_group_id),
setNames(zt_group.import$shape, zt_group.import$zt_group_id))
names(zt_group_id) <- c("col", "en", "dt", "shape")
mclust.import <- dbGetQuery(con,
"select * from cau.mclust")
mclust <- list(
setNames(mclust.import$color, mclust.import$mclust),
setNames(mclust.import$mclust_en, mclust.import$mclust),
setNames(mclust.import$mclust_dt, mclust.import$mclust),
setNames(mclust.import$shape, mclust.import$mclust)
)
names(mclust) <- c("col", "en", "dt", "shape")
mclust_group.import <- dbGetQuery(con,
"select * from cau.mclust_group")
mclust_group <- list(
setNames(mclust_group.import$color, mclust_group.import$mclust_group),
setNames(mclust_group.import$mclust_group_en, mclust_group.import$mclust_group),
setNames(mclust_group.import$mclust_group_dt, mclust_group.import$mclust_group),
setNames(mclust_group.import$shape, mclust_group.import$mclust_group)
)
names(mclust_group) <- c("col", "en", "dt", "shape")
mountain.import <- dbGetQuery(con,
"select * from ore.mountain")
mountain_id <- list(
setNames(mountain.import$color, mountain.import$mountain_id),
setNames(mountain.import$mountain, mountain.import$mountain_id),
setNames(mountain.import$mountain, mountain.import$mountain_id)
)
names(mountain_id) <- c("col", "en", "dt")
}
#Import Datasets----
{
##Import Sites----
{
sites <- st_read(con,
query =
"
select site_id, site_dt, culture_id, culture_en, region_id, region_en, zt_id, zt_en, min, max, geography, sn1, sn2, pb1, pb2, zn1, zn2, bi1, bi2, ag1, ag2, sb1, sb2, as1, as2, fe1, fe2, ni1, ni2, co1, co2, au1, au2
from cau.site join cau.find using (site_id) join cau.feature using (site_id, feature_id) join cau.geography using (geography_id) join cau.zt using (zt_id) join cau.culture using (culture_id) join cau.region using (region_id) left join cau.ca_zt using (site_id, zt_id)
where region_id=1 or region_id = 2 or region_id = 3 or region_id = 4 or region_id = 5 or region_id = 6 or region_id = 17 or region_id = 18 or region_id = 19 or region_id = 20 or region_id = 21 or region_id = 22 or region_id = 23 or region_id = 24 or region_id = 26
group by site_id, site_dt, culture_id, culture_en, region_id, region_en, zt_id, zt_en, min, max, geography, sn1, sn2, pb1, pb2, zn1, zn2, bi1, bi2, ag1, ag2, sb1, sb2, as1, as2, fe1, fe2, ni1, ni2, co1, co2, au1, au2;
")
sites$lng <- as.data.frame((st_coordinates(sites)))$X
sites$lat <- as.data.frame((st_coordinates(sites)))$Y
sites <- rename(sites, region=region_en)
sites <- rename(sites, culture=culture_en)
sites <- rename(sites, zt=zt_en)
sites <- merge(sites,
data.frame(culture_id = names(culture_id$col), col = unname(culture_id$col)),
by= "culture_id")
sites <- rename(sites, Sn1 = sn1)
sites <- rename(sites, Pb1 = pb1)
sites <- rename(sites, Zn1 = zn1)
sites <- rename(sites, Bi1 = bi1)
sites <- rename(sites, Ag1 = ag1)
sites <- rename(sites, Sb1 = sb1)
sites <- rename(sites, As1 = as1)
sites <- rename(sites, Fe1 = fe1)
sites <- rename(sites, Ni1 = ni1)
sites <- rename(sites, Co1 = co1)
sites <- rename(sites, Au1 = au1)
sites <- rename(sites, Sn2 = sn2)
sites <- rename(sites, Pb2 = pb2)
sites <- rename(sites, Zn2 = zn2)
sites <- rename(sites, Bi2 = bi2)
sites <- rename(sites, Ag2 = ag2)
sites <- rename(sites, Sb2 = sb2)
sites <- rename(sites, As2 = as2)
sites <- rename(sites, Fe2 = fe2)
sites <- rename(sites, Ni2 = ni2)
sites <- rename(sites, Co2 = co2)
sites <- rename(sites, Au2 = au2)
sites$Cu1 <- replace_na(sites$Cu1, 0.001)
sites$Sn1 <- replace_na(sites$Sn1, 0.001)
sites$Pb1 <- replace_na(sites$Pb1, 0.001)
sites$Zn1 <- replace_na(sites$Zn1, 0.001)
sites$Bi1 <- replace_na(sites$Bi1, 0.001)
sites$Ag1 <- replace_na(sites$Ag1, 0.001)
sites$Sb1 <- replace_na(sites$Sb1, 0.001)
sites$As1 <- replace_na(sites$As1, 0.001)
sites$Fe1 <- replace_na(sites$Fe1, 0.001)
sites$Co1 <- replace_na(sites$Co1, 0.001)
sites$Ni1 <- replace_na(sites$Ni1, 0.001)
sites$Au1 <- replace_na(sites$Au1, 0.001)
sites$Sn1[sites$Sn1==0] <- 0.001
sites$Pb1[sites$Pb1==0] <- 0.001
sites$Zn1[sites$Zn1==0] <- 0.001
sites$Bi1[sites$Bi1==0] <- 0.001
sites$Ag1[sites$Ag1==0] <- 0.001
sites$Sb1[sites$Sb1==0] <- 0.001
sites$As1[sites$As1==0] <- 0.001
sites$Fe1[sites$Fe1==0] <- 0.001
sites$Co1[sites$Co1==0] <- 0.001
sites$Ni1[sites$Ni1==0] <- 0.001
sites$Au1[sites$Au1==0] <- 0.001
sites$Sn1[sites$Sn1==0.0001] <- 0.001
sites$Pb1[sites$Pb1==0.0001] <- 0.001
sites$Zn1[sites$Zn1==0.0001] <- 0.001
sites$Bi1[sites$Bi1==0.0001] <- 0.001
sites$Ag1[sites$Ag1==0.0001] <- 0.001
sites$Sb1[sites$Sb1==0.0001] <- 0.001
sites$As1[sites$As1==0.0001] <- 0.001
sites$Fe1[sites$Fe1==0.0001] <- 0.001
sites$Co1[sites$Co1==0.0001] <- 0.001
sites$Ni1[sites$Ni1==0.0001] <- 0.001
sites$Au1[sites$Au1==0.0001] <- 0.001
sites$Sn2 <- replace_na(sites$Sn2, 0.001)
sites$Pb2 <- replace_na(sites$Pb2, 0.001)
sites$Zn2 <- replace_na(sites$Zn2, 0.001)
sites$Bi2 <- replace_na(sites$Bi2, 0.001)
sites$Ag2 <- replace_na(sites$Ag2, 0.001)
sites$Sb2 <- replace_na(sites$Sb2, 0.001)
sites$As2 <- replace_na(sites$As2, 0.001)
sites$Fe2 <- replace_na(sites$Fe2, 0.001)
sites$Co2 <- replace_na(sites$Co2, 0.001)
sites$Ni2 <- replace_na(sites$Ni2, 0.001)
sites$Au2 <- replace_na(sites$Au2, 0.001)
sites$Sn2[sites$Sn2==0] <- 0.001
sites$Pb2[sites$Pb2==0] <- 0.001
sites$Zn2[sites$Zn2==0] <- 0.001
sites$Bi2[sites$Bi2==0] <- 0.001
sites$Ag2[sites$Ag2==0] <- 0.001
sites$Sb2[sites$Sb2==0] <- 0.001
sites$As2[sites$As2==0] <- 0.001
sites$Fe2[sites$Fe2==0] <- 0.001
sites$Co2[sites$Co2==0] <- 0.001
sites$Ni2[sites$Ni2==0] <- 0.001
sites$Au2[sites$Au2==0] <- 0.001
sites$Sn2[sites$Sn2==0.0001] <- 0.001
sites$Pb2[sites$Pb2==0.0001] <- 0.001
sites$Zn2[sites$Zn2==0.0001] <- 0.001
sites$Bi2[sites$Bi2==0.0001] <- 0.001
sites$Ag2[sites$Ag2==0.0001] <- 0.001
sites$Sb2[sites$Sb2==0.0001] <- 0.001
sites$As2[sites$As2==0.0001] <- 0.001
sites$Fe2[sites$Fe2==0.0001] <- 0.001
sites$Co2[sites$Co2==0.0001] <- 0.001
sites$Ni2[sites$Ni2==0.0001] <- 0.001
sites$Au2[sites$Au2==0.0001] <- 0.001
sites <- rename(sites, site=site_dt)
elements <- names(ca[23:33])
}
#Import CA ----
{
ca <- dbGetQuery(con,
"
SELECT find_id, part_id, site_id, site_dt, ca_id, culture_id, culture_en, zt_id, zt_group_id, region_id, region_en, min, max, find_character_id, find_character_en, type_id, main_id, mclust, mclust_group, clust_hard, clust_col, cu, sn, pb, zn, bi, ag, sb, ars, fe, ni, co, au
FROM cau.ca JOIN cau.find USING (find_id, site_id) JOIN cau.mclust USING (mclust) JOIN cau.feature USING (feature_id, site_id) join cau.site using (site_id) join cau.zt using (zt_id) join cau.culture using (culture_id) join cau.region using (region_id) join cau.find_character using (find_character_id)
WHERE main_id=1 and (region_id=1 or region_id = 2 or region_id = 3 or region_id = 4 or region_id = 5 or region_id = 6 or region_id = 17 or region_id = 18 or region_id = 19 or region_id = 20 or region_id = 21 or region_id = 22 or region_id = 23 or region_id = 24 or region_id = 26)
GROUP BY find_id, part_id, site_id, site_dt, ca_id, culture_id, culture_en, zt_id, zt_group_id, region_id, region_en, min, max, find_character_id, find_character_en, type_id, main_id, mclust, mclust_group, clust_hard, clust_col, cu, sn, pb, zn, bi, ag, sb, ars, fe, ni, co, au;
")
ca <- rename(ca, region=region_en)
ca <- rename(ca, culture=culture_en)
ca <- rename(ca, find_character=find_character_en)
ca <- rename(ca, site=site_dt)
ca <- rename(ca, Cu = cu)
ca <- rename(ca, Sn = sn)
ca <- rename(ca, Pb = pb)
ca <- rename(ca, Zn = zn)
ca <- rename(ca, Bi = bi)
ca <- rename(ca, Ag = ag)
ca <- rename(ca, Sb = sb)
ca <- rename(ca, As = ars)
ca <- rename(ca, Fe = fe)
ca <- rename(ca, Ni = ni)
ca <- rename(ca, Co = co)
ca <- rename(ca, Au = au)
ca$culture_id <- as.character(ca$culture_id)
ca$find_character_id <- as.character(ca$find_character_id)
ca$zt_id <- as.character(ca$zt_id)
ca$region_id <- as.character(ca$region_id)
ca$mclust <- as.factor(ca$mclust)
ca$mclust_group <- as.factor(ca$mclust_group)
ca$clust_hard <- as.factor(ca$clust_hard)
ca$clust_col <- as.factor(ca$clust_col)
ca$zt_group_id <- as.factor(ca$zt_group_id)
ca$Cu <- replace_na(ca$Cu, 0.001)
ca$Sn <- replace_na(ca$Sn, 0.001)
ca$Pb <- replace_na(ca$Pb, 0.001)
ca$Zn <- replace_na(ca$Zn, 0.001)
ca$Bi <- replace_na(ca$Bi, 0.001)
ca$Ag <- replace_na(ca$Ag, 0.001)
ca$Sb <- replace_na(ca$Sb, 0.001)
ca$As <- replace_na(ca$As, 0.001)
ca$Fe <- replace_na(ca$Fe, 0.001)
ca$Co <- replace_na(ca$Co, 0.001)
ca$Ni <- replace_na(ca$Ni, 0.001)
ca$Au <- replace_na(ca$Au, 0.001)
ca$Cu[ca$Cu==0] <- 0.001
ca$Sn[ca$Sn==0] <- 0.001
ca$Pb[ca$Pb==0] <- 0.001
ca$Zn[ca$Zn==0] <- 0.001
ca$Bi[ca$Bi==0] <- 0.001
ca$Ag[ca$Ag==0] <- 0.001
ca$Sb[ca$Sb==0] <- 0.001
ca$As[ca$As==0] <- 0.001
ca$Fe[ca$Fe==0] <- 0.001
ca$Co[ca$Co==0] <- 0.001
ca$Ni[ca$Ni==0] <- 0.001
ca$Au[ca$Au==0] <- 0.001
ca$Cu[ca$Cu==0.0001] <- 0.001
ca$Sn[ca$Sn==0.0001] <- 0.001
ca$Pb[ca$Pb==0.0001] <- 0.001
ca$Zn[ca$Zn==0.0001] <- 0.001
ca$Bi[ca$Bi==0.0001] <- 0.001
ca$Ag[ca$Ag==0.0001] <- 0.001
ca$Sb[ca$Sb==0.0001] <- 0.001
ca$As[ca$As==0.0001] <- 0.001
ca$Fe[ca$Fe==0.0001] <- 0.001
ca$Co[ca$Co==0.0001] <- 0.001
ca$Ni[ca$Ni==0.0001] <- 0.001
ca$Au[ca$Au==0.0001] <- 0.001
}
#Import-Pb----
{
pb <- dbGetQuery(con,
"SELECT find_id, part_id, site_id, site_dt, ca_id, culture_id, culture_en, zt_id, zt_group_id, region_id, region_en, min, max, find_character_id, find_character_en, type_id, main_id, mclust, mclust_group, clust_hard, clust_col, cu, sn, pb, zn, bi, ag, sb, ars, fe, ni, co, au, pb206_204, pb207_204, pb208_204, pb207_206, pb208_206
FROM cau.pb join cau.ca using (site_id, find_id, part_id) JOIN cau.find USING (find_id, site_id) JOIN cau.mclust USING (mclust) JOIN cau.feature USING (feature_id, site_id) join cau.site using (site_id) join cau.zt using (zt_id) join cau.culture using (culture_id) join cau.region using (region_id) join cau.find_character using (find_character_id)
WHERE main_id=1 and (region_id=1 or region_id = 2 or region_id = 3 or region_id = 4 or region_id = 5 or region_id = 6 or region_id = 17 or region_id = 18 or region_id = 19 or region_id = 20 or region_id = 21 or region_id = 22 or region_id = 23 or region_id = 24 or region_id = 26)
GROUP BY find_id, part_id, site_id, site_dt, ca_id, culture_id, culture_en, zt_id, zt_group_id, region_id, region_en, min, max, find_character_id, find_character_en, type_id, main_id, mclust, mclust_group, clust_hard, clust_col, cu, sn, pb, zn, bi, ag, sb, ars, fe, ni, co, au, pb206_204, pb207_204, pb208_204, pb207_206, pb208_206;
")
pb <- rename(pb, region=region_en)
pb <- rename(pb, culture=culture_en)
pb <- rename(pb, find_character=find_character_en)
pb <- rename(pb, site=site_dt)
pb <- rename(pb, Cu = cu)
pb <- rename(pb, Sn = sn)
pb <- rename(pb, Pb = pb)
pb <- rename(pb, Zn = zn)
pb <- rename(pb, Bi = bi)
pb <- rename(pb, Ag = ag)
pb <- rename(pb, Sb = sb)
pb <- rename(pb, As = ars)
pb <- rename(pb, Fe = fe)
pb <- rename(pb, Ni = ni)
pb <- rename(pb, Co = co)
pb <- rename(pb, Au = au)
pb$culture_id <- as.character(pb$culture_id)
pb$find_character_id <- as.character(pb$find_character_id)
pb$zt_id <- as.character(pb$zt_id)
pb$region_id <- as.character(pb$region_id)
pb$mclust <- as.factor(pb$mclust)
pb$mclust_group <- as.factor(pb$mclust_group)
pb$clust_hard <- as.factor(pb$clust_hard)
pb$clust_col <- as.factor(pb$clust_col)
pb$zt_group_id <- as.factor(pb$zt_group_id)
pb$Cu <- replace_na(pb$Cu, 0.001)
pb$Sn <- replace_na(pb$Sn, 0.001)
pb$Pb <- replace_na(pb$Pb, 0.001)
pb$Zn <- replace_na(pb$Zn, 0.001)
pb$Bi <- replace_na(pb$Bi, 0.001)
pb$Ag <- replace_na(pb$Ag, 0.001)
pb$Sb <- replace_na(pb$Sb, 0.001)
pb$As <- replace_na(pb$As, 0.001)
pb$Fe <- replace_na(pb$Fe, 0.001)
pb$Co <- replace_na(pb$Co, 0.001)
pb$Ni <- replace_na(pb$Ni, 0.001)
pb$Au <- replace_na(pb$Au, 0.001)
pb$Cu[pb$Cu==0] <- 0.001
pb$Sn[pb$Sn==0] <- 0.001
pb$Pb[pb$Pb==0] <- 0.001
pb$Zn[pb$Zn==0] <- 0.001
pb$Bi[pb$Bi==0] <- 0.001
pb$Ag[pb$Ag==0] <- 0.001
pb$Sb[pb$Sb==0] <- 0.001
pb$As[pb$As==0] <- 0.001
pb$Fe[pb$Fe==0] <- 0.001
pb$Co[pb$Co==0] <- 0.001
pb$Ni[pb$Ni==0] <- 0.001
pb$Au[pb$Au==0] <- 0.001
pb$Cu[pb$Cu==0.0001] <- 0.001
pb$Sn[pb$Sn==0.0001] <- 0.001
pb$Pb[pb$Pb==0.0001] <- 0.001
pb$Zn[pb$Zn==0.0001] <- 0.001
pb$Bi[pb$Bi==0.0001] <- 0.001
pb$Ag[pb$Ag==0.0001] <- 0.001
pb$Sb[pb$Sb==0.0001] <- 0.001
pb$As[pb$As==0.0001] <- 0.001
pb$Fe[pb$Fe==0.0001] <- 0.001
pb$Co[pb$Co==0.0001] <- 0.001
pb$Ni[pb$Ni==0.0001] <- 0.001
pb$Au[pb$Au==0.0001] <- 0.001
}
##Import ore ----
{
ore <- dbGetQuery(con,
"select inv, material, site, mountain_id, region, pb206_204, pb207_204, pb208_204
from ore.pb join ore.site using (site_id) join ore.mountain using (mountain_id) join ore.region using (region_id) join ore.material using (material_id)
group by inv, material, site, mountain_id, region, pb206_204, pb207_204, pb208_204;")
ore$mountain_id <- as.factor(ore$mountain_id)
}
}
#Functions----
{
desginLegend <- function()
{
guides(color=guide_legend(title=NULL, nrow=3, byrow=TRUE), shape=guide_legend(title=NULL, nrow=3, byrow=TRUE), fill=guide_legend(title=NULL, nrow=3, byrow=TRUE))
}
##Basic Diagramms----
{
scatter <- function(data, x, y, var)
{
ggplot(
data = data, aes(x = .data[[x]], y = .data[[y]])) +
geom_point(
aes(color={{var}}, shape={{var}})) +
coord_fixed(ratio = 1) +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal") +
desginLegend() +
scale_color_manual(values = c(var$col), labels = c(var$en), limits = force) +
scale_shape_manual(values = c(var$shape), labels = c(var$en), limits = force)
}
scatter_dlog <- function(data, x, y, var)
{
ggplot(
data = data, aes(x = .data[[x]], y = .data[[y]])) +
geom_point(
aes(color={{var}}, shape={{var}})) +
coord_fixed(ratio = 1) +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal") +
desginLegend() +
scale_color_manual(values = c(var$col), labels = c(var$en), limits = force) +
scale_shape_manual(values = c(var$shape), labels = c(var$en), limits = force) +
scale_x_log10() + scale_y_log10()
}
histo <- function(data, x, var, bin)
{
ggplot(
data = data, aes(x = .data[[x]])) +
geom_histogram(binwidth = bin,
aes(fill={{var}})) +
theme_bw() +
theme(legend.position = "bottom", legend.direction = "horizontal") +
desginLegend() +
scale_fill_manual(values = c(var$col), labels = c(var$en), limits = force)
}
histo_log <- function(data, x, var, bin)
{
ggplot(
data = data, aes(x = .data[[x]])) +
geom_histogram(binwidth = bin,
aes(fill={{var}})) +
scale_x_log10() +
theme_bw() +
theme(legend.position = "none") +
desginLegend() +
scale_fill_manual(values = c(var$col), labels = c(var$en), limits = force)
}
histo_log_fac <- function(data, x, var, bin, fac)
{
ggplot(
data = data, aes(x = .data[[x]])) +
geom_histogram(binwidth = bin,
aes(fill={{var}})) +
scale_x_log10() +
theme_bw() +
theme(legend.position = "none") +
desginLegend() +
scale_fill_manual(values = c(var$col), labels = c(var$en), limits = force) +
facet_grid(rows = vars({{fac}}), scales = "free", labeller = labeller(.rows = c(fac$en)))
}
histo_fac <- function(data, x, var, bin, fac)
{
ggplot(
data = data, aes(x = .data[[x]])) +
geom_histogram(binwidth = bin,
aes(fill={{var}})) +
theme_bw() +
theme(legend.position = "none") +
desginLegend() +
scale_fill_manual(values = c(var$col), labels = c(var$en), limits = force) +
facet_grid(rows = vars({{fac}}), scales = "free", labeller = labeller(.rows = c(fac$en)))
}
box_log <- function(data, x, var)
{
ggplot(
data = data, aes(x = .data[[x]])) +
geom_boxplot(
aes(fill={{var}})) +
scale_x_log10() +
theme_bw() +
guides(fill=guide_legend(title=NULL))+
scale_fill_manual(values = c(var$col), labels = c(var$en), limits = force)
}
box <- function(data, x, var)
{
ggplot(
data = data, aes(x = .data[[x]])) +
geom_boxplot(
aes(fill={{var}})) +
theme_bw() +
guides(fill=guide_legend(title=NULL))+
scale_fill_manual(values = c(var$col), labels = c(var$en), limits = force)
}
bar <- function(data, x, var)
{
ggplot(
data = data, aes(.data[[x]])) +
geom_bar(aes(fill={{var}})) +
theme_bw() +
theme(legend.position = "none", strip.text.y = element_text(angle = 0)) +
desginLegend() +
scale_fill_manual(values = c(var$col), labels = c(var$en), limits = force) +
scale_x_discrete(labels = c(var$en))
}
bar_facet <- function(data, x, var, fac)
{
ggplot(
data = data, aes(.data[[x]])) +
geom_bar(aes(fill={{var}})) +
theme_bw() +
theme(legend.position = "none", strip.text.y = element_text(angle = 0)) +
desginLegend() +
scale_fill_manual(values = c(var$col), limits = force) +
scale_x_discrete(labels = c(get(x)$en)) +
facet_grid(rows = vars({{fac}}), scales = "free", labeller = labeller(.rows = c(fac$en)))
}
##Pb-isotope-diagramms----
{
diagramm_pb_207 <- function(data, var)
{
ggplot(data=data, aes(x=pb206_204, y=pb207_204)) +
geom_point(
aes(color={{var}}, shape={{var}})) +
coord_fixed(ratio = 1) +
xlab(expression(frac(Pb[206],Pb[204]))) + ylab(expression(frac(Pb[207],Pb[204]))) +
theme_bw() +
desginLegend() +
scale_color_manual(values = c(var$col), labels = c(var$en), limits = force) +
scale_shape_manual(values = c(var$shape), labels = c(var$en), limits = force)
}
diagramm_pb_208 <- function(data, var)
{
ggplot(data=data, aes(x=pb206_204, y=pb208_204)) +
geom_point(
aes(color={{var}}, shape={{var}})) +
coord_fixed(ratio = 1) +
xlab(expression(frac(Pb[206],Pb[204]))) + ylab(expression(frac(Pb[208],Pb[204]))) +
theme_bw() +
desginLegend() +
scale_color_manual(values = c(var$col), labels = c(var$en), limits = force) +
scale_shape_manual(values = c(var$shape), labels = c(var$en), limits = force)
}
}
##Pb-isotope-diagramms----
{
diagramm_pb_207mod <- function(dataPb, varPb, dataOre, varOre)
{
ggplot(data=NULL, aes(x=pb206_204, y=pb207_204)) +
stat_bin_hex(data = dataOre,
aes(fill={{varOre}})) +
scale_fill_manual(values = c(varOre$col), labels = c(varOre$en), limits = force) +
new_scale_fill() +
geom_point(data = dataPb,
aes(fill={{varPb}}, shape={{varPb}})) +
scale_fill_manual(values = c(varPb$col), labels = c(varPb$en), limits = force) +
scale_shape_manual(values = c(varPb$shape), labels = c(varPb$en), limits = force) +
xlab(expression(frac(Pb[206],Pb[204]))) + ylab(expression(frac(Pb[207],Pb[204]))) +
theme_bw() +
theme(axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.x = element_blank(),
plot.margin = unit(c(5.5, 5.5, 0, 5.5), "pt")
) +
coord_fixed(ratio = 1) +
desginLegend()
}
diagramm_pb_208mod <- function(dataPb, varPb, dataOre, varOre)
{
ggplot(data=NULL, aes(x=pb206_204, y=pb208_204)) +
stat_bin_hex(data = dataOre,
aes(fill={{varOre}})) +
scale_fill_manual(values = c(varOre$col), labels = c(varOre$en), limits = force) +
new_scale_fill() +
geom_point(data = dataPb,
aes(fill={{varPb}}, shape={{varPb}})) +
scale_fill_manual(values = c(varPb$col), labels = c(varPb$en), limits = force) +
scale_shape_manual(values = c(varPb$shape), labels = c(varPb$en), limits = force) +
xlab(expression(frac(Pb[206],Pb[204]))) + ylab(expression(frac(Pb[207],Pb[204]))) +
theme_bw() +
theme(plot.margin = unit(c(5.5, 5.5, 0, 5.5), "pt")) +
coord_fixed(ratio = 1) +
desginLegend()
}
}
##Admixture-diagramm----
{
##1/Pb-isotope-diagramm----
diagramm_1_pb_206 <- function(data, x, var)
{
ggplot(
data = data, aes(x=1/{{x}}, y=pb206_204)) +
geom_point(
aes(color={{var}}, shape={{var}})) +
scale_x_log10() +
ylab(expression(frac(Pb[206],Pb[204]))) +
theme_bw() +
desginLegend() +
scale_color_manual(values = c(var$col), labels = c(var$en), limits = force) +
scale_shape_manual(values = c(var$shape), labels = c(var$en), limits = force)
}
diagramm_1_pb_207 <- function(data, x, var)
{
ggplot(
data = data, aes(x=1/{{x}}, y=pb207_204)) +
geom_point(
aes(color={{var}}, shape={{var}})) +
scale_x_log10() +
ylab(expression(frac(Pb[207],Pb[204]))) +
theme_bw() +
desginLegend() +
scale_color_manual(values = c(var$col), labels = c(var$en), limits = force) +
scale_shape_manual(values = c(var$shape), labels = c(var$en), limits = force)
}
diagramm_1_pb_208 <- function(data, x, var)
{
ggplot(
data = data, aes(x=1/{{x}}, y=pb208_204)) +
geom_point(
aes(color={{var}}, shape={{var}})) +
scale_x_log10() +
ylab(expression(frac(Pb[208],Pb[204]))) +
theme_bw() +
desginLegend() +
scale_color_manual(values = c(var$col), labels = c(var$en), limits = force) +
scale_shape_manual(values = c(var$shape), labels = c(var$en), limits = force)
}
##x/Pb-isotope-diagramms----
diagramm_el_pb_206 <- function(data, x, var)
{
ggplot(
data = data, aes(x={{x}}/Pb, y=pb206_204)) +
geom_point(size = 2,
aes(color={{var}}, shape={{var}}, shape={{var}})) +
scale_x_log10() +
ylab(expression(frac(Pb[206],Pb[204]))) +
theme_bw() +
desginLegend() +
scale_color_manual(values = c(var$col), labels = c(var$en), limits = force) +
scale_shape_manual(values = c(var$shape), labels = c(var$en), limits = force)
}
diagramm_el_pb_207 <- function(data, x, var)
{
ggplot(
data = data, aes(x={{x}}/Pb, y=pb207_204)) +
geom_point(size = 2,
aes(color={{var}}, shape={{var}})) +
scale_x_log10() +
ylab(expression(frac(Pb[207],Pb[204]))) +
theme_bw() +
desginLegend() +
scale_color_manual(values = c(var$col), labels = c(var$en), limits = force) +
scale_shape_manual(values = c(var$shape), labels = c(var$en), limits = force)
}
diagramm_el_pb_208 <- function(data, x, var)
{
ggplot(
data = data, aes(x={{x}}/Pb, y=pb208_204)) +
geom_point(size = 2,
aes(color={{var}}, shape={{var}})) +
scale_x_log10() +
ylab(expression(frac(Pb[208],Pb[204]))) +
theme_bw() +
desginLegend() +
scale_color_manual(values = c(var$col), labels = c(var$en), limits = force) +
scale_shape_manual(values = c(var$shape), labels = c(var$en), limits = force)
}
}
}
##UI-elements ----
{
histoDropdownButton <- function(inputId1, inputId2, inputId3)
{dropdownButton(
noUiSliderInput(inputId1,
max = 1,
min = 0.1,
value = 0.1,
step = 0.1,
label = "Diagramm Binwidth"),
selectInput(inputId2,
label = "Element",
choices = names(ca[elements])
),
selectInput(inputId3,
label = "Scale",
choices = c(
"normal" = "contx",
"logarithmic" = "logx"
)
),
circle = TRUE,
width = "300px",
size = "sm",
tooltip = tooltipOptions(title = "Click to see inputs !")
)}
scatterDropdownButton <- function(inputIdx, inputIdy)
{dropdownButton(
selectInput(inputIdx,
label = "Element",
choices = names(ca[elements])
),
selectInput(inputIdy,
label = "Element",
choices = names(ca[elements])
),
circle = TRUE,
width = "300px",
size = "sm",
tooltip = tooltipOptions(title = "Click to see inputs !")
)}
barDropdownButton <- function(inputIdx, inputIdy)
{dropdownButton(
selectInput(inputIdx,
label = "x-Axis",
choices = variab
),
selectInput(inputIdy,
label = "Rows",
choices = variab
),
circle = TRUE,
width = "300px",
size = "sm",
tooltip = tooltipOptions(title = "Click to see inputs !")
)}
designSliders <- function(inputId1, inputId2, number)
{
fluidRow(
column(6,
noUiSliderInput(inputId1,
max = 250,
min = 35,
value = 100,
step = 5,
label = "Diagramm Resulution")
),
column(6,
noUiSliderInput(inputId2,
max = 1000,
min = 200,
value = number,
step = 10,
label = "Diagramm Size")
)
)
}
elementSlider <- function(InputId)
{
sliderTextInput(InputId,
choices = c(0.001, 0.01, 0.1, 1, 10, 100),
label = InputId,
grid = TRUE,
selected = c(0.001, 100))
}
swap <- function(data)
{
setNames(names(data),data)
}
minMaxInput <- function(inputId)
{
splitLayout(cellWidths = c("10%", "45%", "45%"), print(inputId), numericInput(paste0(inputId, 1), label=NULL, value = 0.001), numericInput(paste0(inputId, 2), label=NULL, value = 100))
}
}
}
#UI----
{
ui <- fluidPage(
sidebarLayout(
##Side-Panel----
{
sidebarPanel(width = 2, height = 12,
noUiSliderInput("range",
max = max(sites$min),
min = min(sites$max),
value=c(min(sites$max),max(sites$min)),
label = "Chronological Range",
step = 10,
direction = "rtl"),
pickerInput("regions",
label = "Regions",
choices = swap(region_id$en),
multiple = TRUE,
selected = unique(ca$region_id),
options = list(
`actions-box` = TRUE)),
pickerInput("cultures",
label = "Cultures",
choices = swap(culture_id$en),
multiple = TRUE,
options = list(
`actions-box` = TRUE)),
pickerInput("periods",
label = "Periods",
choices = swap(zt_id$en),
multiple = TRUE,
options = list(
`live-search` = TRUE,
`actions-box` = TRUE)),
pickerInput("sites",
label = "Sites",
choices = swap(site_id$en),
multiple = TRUE,
options = list(
`live-search` = TRUE,
`actions-box` = TRUE)),
pickerInput("mclust",
label = "Cluster",
choices = swap(mclust$en),
multiple = TRUE,
options = list(
`live-search` = TRUE,
`actions-box` = TRUE)),
pickerInput("mclust_group",
label = "Cluster-Groups",
choices = swap(mclust_group$en),
multiple = TRUE,
options = list(
`live-search` = TRUE,
`actions-box` = TRUE)),
pickerInput("mountains",
label = "Mountain range",
choices = swap(mountain_id$en),
multiple = TRUE,
options = list(
`live-search` = TRUE,
`actions-box` = TRUE)),
pickerInput("inputVar",
label = "Variable",
choices = variab),
pickerInput("find_character",
label = "Typological Groups",
choices = unique((arrange(ca, find_character)$find_character)),
multiple = TRUE,
options = list(
`actions-box` = TRUE)),
map(elements , ~minMaxInput(.x))
)
},
#Main Panel----
{
mainPanel(width = 10, height = 12,
navbarPage("Archmetal",
###Map----
{
tabPanel("Map", leafletOutput("map", width = "100%", height = 900))
},
##Scatter-Plots----
{
navbarMenu("Scatter-Plots",
tabPanel("Single Plot",
fluidRow(
column(12, align = "center",
plotOutput("c_legend", height = heightLegend)
)
),
fluidRow(
column(12, align = "center",
scatterDropdownButton("xc1", "yc1"),
plotOutput("c1",
height = "100%"
)
)
),
designSliders("resols1", "sizes1", 700)
),
tabPanel("Two Plots",
fluidRow(
column(12, align = "center",
plotOutput("f_legend", height = heightLegend))
),
fluidRow(
column(6, align = "center",
scatterDropdownButton("xf1", "yf1"),
plotOutput("f1", width = "100%", height = "100%")),
column(6, align = "center",
scatterDropdownButton("xf2", "yf2"),
plotOutput("f2", width = "100%", height = "100%"))
),
designSliders("resols2", "sizes2", 700)
),
tabPanel("Four Plots",
fluidRow(
column(12, align = "center",
plotOutput("r_legend", height = heightLegend))
),