I would like to use different colors for specific ranges of values a have in grids in a map (Southern Hemisphere), when working with this dataset. I'm not sure if have defined to blocks correctly and I don't know how to ask for different colors for each block where I have at least one occurrence.
I'm using ggplot2 in R to create a map with grids with different numbers of individuals in each. I got a nice plot, but it is showing me only few colors/shades (because I have few grids with high values). So I divided the range of the individuals sighted in each grid (n, that varies from 1-15035) in blocks (by = 100) to then ask R to use a different color/shades considering the block that each grid belongs to (e.g. use one color for the grids where I have 1-100 individuals, another color for the ones with 101-200 individuals, and so on). I know that I have many (151) blocks, but from them there's only 30 where a have at least one occurrence (there's no grid with most of the ranges). There's a mistake in my blocks (breaks in the code provided, as there's some overlap) and I don't know how to include this information when creating the plot to ask for the 30 different colors for each of the blocks where the frequency is different from zero. I tried some options using the ggplot arguments there I kept in the code provided here (the first three lines creating a object 'sc'). How should I specify my blocks (breaks) to avoid the overlap I'm getting? Is the limits argument right in the code? How to ask for different colors for the blocks where I have at least one individuals (n>0)?
Any tip will be very appreciated :)
##Setting workspace
#setwd...
rm(list=ls()) #removing previous objects
#Installing (or loading) necessary packages
packages = c('ggplot2','sp','rgdal','sf','readxl','maps','dplyr')
package.check = lapply(packages, FUN = function(x) {
if (!require(x, character.only = TRUE)) {
install.packages(x, dependencies = TRUE)
library(x, character.only = TRUE)
}
})
#### Data ###
hump = read_excel("data_r.xlsx")
range(hump$Lat_Dec)
range(hump$Lon_Dec)
#Convert df to sf -----------------------------
hbk_sf = st_as_sf(x = hump,
coords = c("Lon_Dec", "Lat_Dec"),
crs = "+init=epsg:4326")
class(hbk_sf)
#Plot
plot(st_geometry(hbk_sf))
#Plot all variables (I don't recommend, it will take some time)
#plot(hbk_sf)
#Create grid--------------
grd = st_make_grid(hbk_sf, cellsize = 10, square = T)
grd = as_Spatial(grd)
grd = st_as_sf(grd)
grd$id = rownames(grd)
class(grd)
#plot(st_geometry(grd),add=T)
#Count individuals at grid------------------
#Spatial join: Add the grid id at hbk dataframe
hbk = st_join(hbk_sf, grd, join = st_within)
range(hbk$id,na.rm=T)
hbk_count = count(as_tibble(hbk), id) #alternativelly hbk_count =
aggregate(hbk$Hbk, by=list(hbk$id), FUN=sum)
hbk_count
#Adding the count in grids
grd_hbk = left_join(grd,hbk_count)
plot(grd_hbk)
range(grd_hbk$n,na.rm=T)
ggplot(grd_hbk,aes(x=n))+geom_density()
#Plotting with ggplot
world = sf::st_as_sf(map('world', plot = FALSE, fill = TRUE))
mymap = ggplot(grd_hbk[!is.na(grd_hbk$n),],aes(fill=n))+
geom_sf(data=world,aes(),fill='grey',lwd=.2)+
geom_sf(alpha=.7,lwd=0)+
scale_fill_distiller(palette = "Spectral")+
coord_sf(crs = st_crs(4326),xlim = c(-165,165), ylim = c(-70,6))+
theme_bw() # + theme(legend.position = 'none')
mymap
mymap = mymap + ggtitle("...")+
theme(plot.title = element_text(color = "black", size = 10, hjust = 0.5))
mymap
ggsave("mymap.png", dpi=300)
#-------
#To give colours to the grids considering the range of catches in each one
#that has at least one catch (grd_hbk>0)
#Tryied to create breaks to then consider in the grd_hbk$n. I wanna R to
#use a different colour/shade considering the range of the grd_hbk$n in
#the grids (one colour for grids with 1-100 catches, another colour for
#grids with 101-200 and so on)---
# Generate breaks to cut the data
breaks = seq(0, 15100, by = 100)
# Cut the data and save the result in an object
r = cut(grd_hbk$n, breaks) #this an overlap (Levels: (0,100] (100,200]
#(200,300]...)
# Check the number of different categories
length(levels(r))
# Name for the levels
levels(r) = as.character(1:152)
#table(levels(r))
table(r)
#create a combination of colours to use in the following plot
#sc = scale_colour_gradientn(colors = 'red', 'blue', 'green')
#sc = scale_fill_grey(start=1, end=15035, aes(fill=y))
#sc = scale_fill_grey(start=min(levels(r)), end=max(levels(r)),
#aes(fill=y))
sc = scale_fill_gradient(low="blue", high="red")
mymapii = ggplot(grd_hbk[!is.na(grd_hbk$n),],aes(fill=n))+
geom_sf(data=world,aes(),fill='grey',lwd=.2)+
geom_sf(alpha=.7,lwd=0)+
scale_colour_manual(limits = min(levels(r)),max(levels(r)),
values = sc, #colors to be used
breaks = breaks,
aes(fill=sc))+ #maybe need another specification here?
coord_sf(crs = st_crs(4326),xlim = c(-165,165), ylim = c(-70,6))+
theme_bw()
mymapii
