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create_plots.R
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create_plots.R
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rm(list = ls())
library(lattice)
library(latticeExtra)
library(maptools)
library(raster)
library(RColorBrewer)
library(tidyverse)
# read data --------------------------------------------------------------------
data_list <- lapply(
FUN = function(i) {
res <- read.table(file = paste0(i, "_data.csv"),
stringsAsFactors = FALSE, header = FALSE)
return(res)
}, X = c("x", "y", "z")
)
names(data_list) <- c("x", "y", "z")
# fix paramates for vizualization ----------------------------------------------
wrld <- maps::map('world', xlim = c(-180, 180),
ylim = c(-90, 90))
wrld <- data.frame(lon = wrld$x, lat = wrld$y)
mycols <- brewer.pal(9, "RdYlBu")[c(-2, -4:-7)]
mybreaks <- c(-2, -0.5, 0, 0.5, 1.5)
# data tarnsformation ----------------------------------------------------------
coord_mx <- t(data_list[["z"]])
df <- as.data.frame(coord_mx, stringsAsFactors = FALSE)
names(df) <- paste0("cn", seq(along.with = df[1, ]))
colnames(df) <- paste0("x_", unlist(data_list[["x"]]))
df[, "y"] <- data_list[["y"]]
df_long <- df %>% pivot_longer(cols = starts_with("x"),
names_to = "x", values_to = "z")
df_long[, "x"] <- as.numeric(gsub(df_long$x,
pattern = "x_", replacement = ""))
data(wrld_simpl)
# note that x and y are reversed
pts <- SpatialPoints(df_long[, c("y", "x")],
proj4string=CRS(proj4string(wrld_simpl)))
# find which points fall over land
ii <- !is.na(over(pts, wrld_simpl)$FIPS)
df_long_clean_ocean <- df_long[ii, ]
# visualization ----------------------------------------------------------------
# image
pdf("image.pdf")
image(x = unlist(data_list$y), y = unlist(data_list$x),
z = t(data_list$z), col = mycols,
zlim = range(data_list$z), useRaster = FALSE,
# main = PlotTit_Text,
breaks = mybreaks,
# sub=PlotInfo,
xlab="",ylab="")
maps::map(database = "world", col="gray25", lwd = 1, add = T,
wrap =c(-180, 180))
fields::image.plot(legend.only = TRUE, zlim= range(data_list$z), col = mycols,
horizontal = TRUE, legend.mar = 2, legend.width = 0.5,
breaks = mybreaks,
panel.first = grid(col = "black"))
dev.off()
# filled.contour() -> filledContour()
pdf("raster_filledCont.pdf")
filledContour(rasterFromXYZ(df_long_clean_ocean), nlevels = 7,
col = mycols)
dev.off()
pdf("raster_filledCont_with_map.pdf")
filledContour(rasterFromXYZ(df_long_clean_ocean), nlevels = 7,
col = mycols)
maps::map("world", add=TRUE)
dev.off()
# ggplot2
map.world <- map_data("world")
ggplot(data = df_long_clean_ocean,
aes(x = y, y = x, z = z, fill = z)) +
geom_tile() +
scale_fill_fermenter(breaks = mybreaks,
palette = "RdYlBu", direction = 1) +
geom_map(dat=map.world, map = map.world, aes(map_id=region),
fill="NA", color="black", inherit.aes = F) +
coord_quickmap() +
labs(x = "long", y = "lat",
fill = "",
title = "",
subtitle = paste0(""),
inherit.aes = FALSE) +
theme(panel.border = element_rect(colour = "gray10",
fill = NA, size = 0.1),
legend.text = element_text(size = 14),
axis.text = element_text(size = 14))
ggsave("ggplot_tile.pdf")
ggplot(data = df_long_clean_ocean,
aes(x = y, y = x, z = z)) +
geom_contour_filled(breaks = mybreaks,
# col = "black",
size = 0.01) +
scale_fill_brewer(palette = "RdYlBu") +
geom_map(dat=map.world, map = map.world, aes(map_id=region),
fill="NA", color="black", inherit.aes = F) +
coord_quickmap() +
labs(x = "long", y = "lat",
fill = "",
title = "",
subtitle = paste0(""),
inherit.aes = FALSE) +
theme(panel.border = element_rect(colour = "gray30",
fill = NA, size = 0.1),
legend.text = element_text(size = 14),
axis.text = element_text(size = 14))
ggsave("ggplot_contour_fill_geo.pdf")
ggplot(data = df_long_clean_ocean,
aes(x = y, y = x, z = z)) +
geom_contour_filled(breaks = c(-2, -0.5, -0.01, 0, 0.01, 0.5, 1.5),
# col = "black",
size = 0.01) +
scale_fill_brewer(palette = "RdYlBu") +
geom_map(dat=map.world, map = map.world, aes(map_id=region),
fill="NA", color="black", inherit.aes = F) +
coord_quickmap() +
labs(x = "long", y = "lat",
fill = "",
title = "",
subtitle = paste0(""),
inherit.aes = FALSE) +
theme(panel.border = element_rect(colour = "gray30",
fill = NA, size = 0.1),
legend.text = element_text(size = 14),
axis.text = element_text(size = 14))
ggsave("ggplot_contour_fill2_geo.pdf")
# lattice
lp <- levelplot(data = df_long_clean_ocean,
z ~ y + x,
pretty = TRUE,
at = mybreaks,
aspect = 1.25,
col.regions = mycols,
contour = TRUE,
# margin = TRUE,
xlab = "", ylab = "")
wp <- xyplot(
data = wrld, lat ~ lon,
lty = 1, lwd = 0.5, fill = 'black', col = 'black', pch = 21,
type = c("l", "g"),
# type = c("l"),
cex = 0.5,
# margin = TRUE,
panel = function(...) {
panel.xyplot(...)
panel.grid(h = -1, v = -1, col.line = "gray10", lwd = 0.5)
}
)
res <- lp + as.layer(wp)
pdf("lattice_cp.pdf")
plot(res)
dev.off()