Convert a raster to a dataframe and extract values you want in R

I want to make a bathymetry map using ggplot2. I converted a raster file to a data frame, clopped and converted it to a dataframe:

library(raster)

##Import a raster file
Bathymetry_dat <- raster("w001000.adf")

##Clop the raster file
Bathy_clopped <- crop(Bathymetry_dat, extent(84.11236, 108.4594, -4.046979, 24.09534))

##Convert it to a dataframe    
datframe_bathy<-as.data.frame(Bathy_clopped, xy = TRUE)

Then, I checked values (i.e. depth in m) in the dataframe:

> summary(datframe_bathy)
       x                y          w001000_COUNT    
 Min.   : 84.11   Min.   :-4.046   Min.   :   9945  
 1st Qu.: 90.20   1st Qu.: 2.987   1st Qu.:  81618  
 Median : 96.28   Median :10.021   Median : 168447  
 Mean   : 96.28   Mean   :10.021   Mean   : 210212  
 3rd Qu.:102.37   3rd Qu.:17.054   3rd Qu.: 336718  
 Max.   :108.45   Max.   :24.087   Max.   :1205362  
                                   NA's   :3449125

Depth (m) values are supposed to be negative and should't be this large. Then, I checked the bathymetry file imported in R.

> Bathy_clopped
class       : RasterLayer 
dimensions  : 3377, 2922, 9867594  (nrow, ncol, ncell)
resolution  : 0.008333333, 0.008333333  (x, y)
extent      : 84.10833, 108.4583, -4.05, 24.09167  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0 
data source : in memory
names       : w001000 
values      : -6138, -1  (min, max)
attributes  :
           ID  COUNT
 from: -11584      1
 to  :     -1 676804

There are two attributes: ID and COUNT. I suppose ID is depth (m) and don't know what COUNT is. And it is weird that COUNT ranges from 1 to 676804 and but summary() shows values from 9945 to 1205362.

So my question is how can I convert a raster file to a dataframe that contains values I want?

With the "COUNT" values, I was able to generate a bathymetry map, but the values in the legend are not correct..

Thanks in advance.

Solution

There is an attribute table with your raster layer. We can use levels to acces it.

library(raster)

# See the attribute table
head(levels(Bathy_clopped)[[1]])
#       ID COUNT
# 1 -11584     1
# 2 -10944     1
# 3 -10907     1
# 4 -10900     1
# 5 -10879     1
# 6 -10878     1

We can then manipulate this attribute table, replacing COUNT with the depth, which is ID.

# Get the attribute table
RAT <- levels(Bathy_clopped)[[1]]

# Replace COUNT with ID
RAT$Depth <- RAT$ID
RAT$COUNT <- NULL

# Replace the attribute table
Bathy_clopped2 <- Bathy_clopped
levels(Bathy_clopped2)[[1]] <- RAT

# Create a single layer based on the new RAT
Bathy_clopped2 <- deratify(Bathy_clopped2)

# Create a data frame
datframe_bathy2 <-as.data.frame(Bathy_clopped2, xy = TRUE)

Now the values in datframe_bathy2 are as expected.

# Summarize the data frame
summary(datframe_bathy2)
#       x                y              COUNT        
# Min.   : 84.11   Min.   :-4.046   Min.   :-6138    
# 1st Qu.: 90.20   1st Qu.: 2.987   1st Qu.:-3800    
# Median : 96.28   Median :10.021   Median :-2428    
# Mean   : 96.28   Mean   :10.021   Mean   :-2154    
# 3rd Qu.:102.37   3rd Qu.:17.054   3rd Qu.:  -65    
# Max.   :108.45   Max.   :24.087   Max.   :   -1    
#                                   NA's   :3449125