Plotting a matrix on ggmap with geom_tile not working - r

Question

I'm trying to plot a matrix (mostly random numbers with a few NAs) with longitude/latitude coordinates on a ggmap plot.
This is my code:
library(ggmap)
library(ggplot2)
define the longitude and latitude coordinates
x1=34.2
x2=42.4
y1=37.4
y2=29.4
lon = seq(x1,x2,by=0.1)
lat = seq(y1,y2,by=-0.1)
define a matrix with random numbers with the longitude/latitude dimensions
set.seed(1)
numbers = rnorm(length(lon)*length(lat))
var = matrix(numbers,length(lon),length(lat))
add some NAs to the matrix
var[1:5,1:5] = NA
lat_min <- min(lat)-0.3
lon_min <- min(lon)-0.3
lat_max <- max(lat)+0.3
lon_max <- max(lon)+0.3
construct the ggmap
map_box <- c(left=lon_min,bottom=lat_min,
right=lon_max,top=lat_max)
total_stmap <- get_stamenmap(bbox=map_box,zoom=5,maptype="toner")
total_ggmap <- ggmap(total_stmap,extent="panel")
make a data.frame to attribute each matrix index to the geographical coordinate
lat_df <- c()
lon_df <- c()
var_df <- c()
for (i in 1:length(lon)) {
for (j in 1:length(lat)) {
lon_df <- c(lon_df,lon[i])
lat_df <- c(lat_df,lat[j])
var_df = var[i,j]
}
}
df=data.frame(Longitude=lon_df,Latitude=lat_df,Variable=var_df)
make the plot using ggmap and geom_tile
plot = total_ggmap +
geom_tile(data=df,aes(x=Longitude,y=Latitude,fill=Variable),alpha=1/2,color="black",size=0) +
geom_sf(data = df, inherit.aes = FALSE, fill = NA)
With this code I get the message:
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
...and a blank plot.

Answer 1

There were two problems here. The first is that all of your values in the Variable column are the same, because you are just overwriting var_df with every iteration of your loop. The line
var_df = var[i,j]
Should be
var_df = c(var_df, var[i,j])
Secondly, you should not be using geom_sf if you have a data frame of longitude, latitude and value. geom_sf is used to plot sf objects, which is not what you have.
Instead, you need only do:
plot <- total_ggmap +
geom_tile(data = df, aes(Longitude, Latitude, fill = Variable), alpha = 1/2, size = 0)
and you get:
plot