Explore and Plot by Vector Layer Attributes
OverviewTeaching: 40 min
Exercises: 20 minQuestions
How can I compute on the attributes of a spatial object?Objectives
Query attributes of a spatial object.
Subset spatial objects using specific attribute values.
Plot a vector feature, colored by unique attribute values.
Things You’ll Need To Complete This Episode
See the lesson homepage for detailed information about the software, data, and other prerequisites you will need to work through the examples in this episode.
This episode continues our discussion of vector layer attributes and covers how to work with vector layer attributes in R. It covers how to identify and query layer attributes, as well as how to subset features by specific attribute values. Finally, we will learn how to plot a feature according to a set of attribute values.
Load the Data
We will continue using the
ggplot2 packages in this episode. Make sure that you have these packages loaded. We will
continue to work with the three shapefiles (vector layers) that we loaded in the
Open and Plot Shapefiles in R episode.
Query Vector Feature Metadata
As we discussed in the Open and Plot Shapefiles in R episode, we can view metadata associated with an R object using:
st_geometry_type()- The type of vector data stored in the object.
nrow()- The number of features in the object
st_bbox()- The spatial extent (geographic area covered by) of the object.
st_crs()- The CRS (spatial projection) of the data.
We started to explore our
point_HARV object in the previous episode.
To see a summary of all of the metadata associated with our
point_HARV object, we can view the object with
View(point_HARV) or print a summary of the object itself to the console.
Simple feature collection with 1 feature and 14 fields geometry type: POINT dimension: XY bbox: xmin: 732183.2 ymin: 4713265 xmax: 732183.2 ymax: 4713265 CRS: 32618 Un_ID Domain DomainName SiteName Type Sub_Type Lat Long 1 A 1 Northeast Harvard Forest Core Advanced Tower 42.5369 -72.17266 Zone Easting Northing Ownership County annotation 1 18 732183.2 4713265 Harvard University, LTER Worcester C1 geometry 1 POINT (732183.2 4713265)
We can use the
ncol function to count the number of attributes associated with a spatial object too. Note that the geometry is just another column and counts towards the total.
We can view the individual name of each attribute using the
names() function in R:
 "OBJECTID_1" "OBJECTID" "TYPE" "NOTES" "MISCNOTES"  "RULEID" "MAPLABEL" "SHAPE_LENG" "LABEL" "BIKEHORSE"  "RESVEHICLE" "RECMAP" "Shape_Le_1" "ResVehic_1" "BicyclesHo"  "geometry"
We could also view just the first 6 rows
of attribute values using the
head() function to get a preview of the data:
Simple feature collection with 6 features and 15 fields geometry type: MULTILINESTRING dimension: XY bbox: xmin: 730741.2 ymin: 4712685 xmax: 732232.3 ymax: 4713726 CRS: 32618 OBJECTID_1 OBJECTID TYPE NOTES MISCNOTES RULEID 1 14 48 woods road Locust Opening Rd <NA> 5 2 40 91 footpath <NA> <NA> 6 3 41 106 footpath <NA> <NA> 6 4 211 279 stone wall <NA> <NA> 1 5 212 280 stone wall <NA> <NA> 1 6 213 281 stone wall <NA> <NA> 1 MAPLABEL SHAPE_LENG LABEL BIKEHORSE RESVEHICLE RECMAP 1 Locust Opening Rd 1297.35706 Locust Opening Rd Y R1 Y 2 <NA> 146.29984 <NA> Y R1 Y 3 <NA> 676.71804 <NA> Y R2 Y 4 <NA> 231.78957 <NA> <NA> <NA> <NA> 5 <NA> 45.50864 <NA> <NA> <NA> <NA> 6 <NA> 198.39043 <NA> <NA> <NA> <NA> Shape_Le_1 ResVehic_1 BicyclesHo 1 1297.10617 R1 - All Research Vehicles Allowed Bicycles and Horses Allowed 2 146.29983 R1 - All Research Vehicles Allowed Bicycles and Horses Allowed 3 676.71807 R2 - 4WD/High Clearance Vehicles Only Bicycles and Horses Allowed 4 231.78962 <NA> <NA> 5 45.50859 <NA> <NA> 6 198.39041 <NA> <NA> geometry 1 MULTILINESTRING ((730819.2 ... 2 MULTILINESTRING ((732040.2 ... 3 MULTILINESTRING ((732057 47... 4 MULTILINESTRING ((731903.6 ... 5 MULTILINESTRING ((732039.1 ... 6 MULTILINESTRING ((732056.2 ...
Challenge: Attributes for Different Spatial Classes
Explore the attributes associated with the
- How many attributes does each have?
- Who owns the site in the
Which of the following is NOT an attribute of the
A) Latitude B) County C) Country
1) To find the number of attributes, we use the
2) Ownership information is in a column named
 "Harvard University, LTER"
3) To see a list of all of the attributes, we can use the
 "Un_ID" "Domain" "DomainName" "SiteName" "Type"  "Sub_Type" "Lat" "Long" "Zone" "Easting"  "Northing" "Ownership" "County" "annotation" "geometry"
“Country” is not an attribute of this object.
Explore Values within One Attribute
We can explore individual values stored within a particular attribute.
Comparing attributes to a spreadsheet or a data frame, this is similar
to exploring values in a column. We did this with the
gapminder dataframe in an earlier lesson. For spatial objects, we can use the same syntax:
We can see the contents of the
TYPE field of our lines feature:
 "woods road" "footpath" "footpath" "stone wall" "stone wall"  "stone wall" "stone wall" "stone wall" "stone wall" "boardwalk"  "woods road" "woods road" "woods road"
To see only unique values within the
TYPE field, we can use the
levels() function for extracting the possible values of a
categorical variable. The special term for categorical variables
within R is factor. We worked with factors a little bit in an earlier lesson.
We can use the
filter() function from
dplyr that we worked with in an earlier lesson to select a subset of features
from a spatial object in R, just like with data frames.
For example, we might be interested only in features that are of
TYPE “footpath”. Once we subset out this data, we can use it as input to other code so that code only operates on the footpath lines.
footpath_HARV <- lines_HARV %>% filter(TYPE == "footpath") nrow(footpath_HARV)
Our subsetting operation reduces the
features count to 2. This means
that only two feature lines in our spatial object have the attribute
TYPE == footpath. We can plot only the footpath lines:
ggplot() + geom_sf(data = footpath_HARV) + ggtitle("NEON Harvard Forest Field Site", subtitle = "Footpaths") + coord_sf()
There are two features in our footpaths subset. Why does the plot look like
there is only one feature? Let’s adjust the colors used in our plot. If we have
2 features in our vector object, we can plot each using a unique color by
assigning a column name to the color aesthetic (
color =). We use the syntax
aes(color = ) to do this. We can also alter the default line thickness by
size = parameter, as the default value of 0.5 can be hard to see.
Note that size is placed outside of the
aes() function, as we are not
connecting line thickness to a data variable.
ggplot() + geom_sf(data = footpath_HARV, aes(color = factor(OBJECTID)), size = 1.5) + labs(color = 'Footpath ID') + ggtitle("NEON Harvard Forest Field Site", subtitle = "Footpaths") + coord_sf()
Now, we see that there are in fact two features in our plot!
Challenge: Subset Spatial Line Objects Part 1
Subset out all
boardwalkfrom the lines layer and plot it.
First we will save an object with only the boardwalk lines:
boardwalk_HARV <- lines_HARV %>% filter(TYPE == "boardwalk")
Let’s check how many features there are in this subset:
Now let’s plot that data:
ggplot() + geom_sf(data = boardwalk_HARV, size = 1.5) + ggtitle("NEON Harvard Forest Field Site", subtitle = "Boardwalks") + coord_sf()
Challenge: Subset Spatial Line Objects Part 2
Subset out all
stone wallfeatures from the lines layer and plot it. For each plot, color each feature using a unique color.
First we will save an object with only the stone wall lines and check the number of features:
stoneWall_HARV <- lines_HARV %>% filter(TYPE == "stone wall") nrow(stoneWall_HARV)
Now we can plot the data:
ggplot() + geom_sf(data = stoneWall_HARV, aes(color = factor(OBJECTID)), size = 1.5) + labs(color = 'Wall ID') + ggtitle("NEON Harvard Forest Field Site", subtitle = "Stonewalls") + coord_sf()
In the examples above,
ggplot() automatically selected colors for
each line based on a default color order. If we don’t like those
default colors, we can create a vector of colors - one for each
feature. To create this vector we can use the following syntax:
c("color_one", "color_two", "color_three")[object$factor]
Note in the above example we have
- a vector of colors - one for each factor value (unique attribute value)
- the attribute itself (
[object$factor]) of class factor.
First we will check how many unique levels our factor has:
Then we can create a palette of four colors, one for each feature in our vector object.
road_colors <- c("blue", "green", "navy", "purple")
We can tell
ggplot to use these colors when we plot the data.
ggplot() + geom_sf(data = lines_HARV, aes(color = TYPE)) + scale_color_manual(values = road_colors) + labs(color = 'Road Type') + ggtitle("NEON Harvard Forest Field Site", subtitle = "Roads & Trails") + coord_sf()
Adjust Line Width
We adjusted line width universally earlier. If we want a unique line width for each factor level or attribute category in our spatial object, we can use the same syntax that we used for colors, above.
We already know that we have four different
TYPE levels in the lines_HARV object, so we will set four different line widths.
line_widths <- c(1, 2, 3, 4)
We can use those line widths when we plot the data.
ggplot() + geom_sf(data = lines_HARV, aes(color = TYPE, size = TYPE)) + scale_color_manual(values = road_colors) + labs(color = 'Road Type') + scale_size_manual(values = line_widths) + ggtitle("NEON Harvard Forest Field Site", subtitle = "Roads & Trails - Line width varies") + coord_sf()
Note that we could also use
aes(size = TYPE) to tie the line thickness to the TYPE variable, so long as we had been careful to set factor levels appropriately. ggplot prints a warning when you do this, because it is not considered a good practice to plot non-spatial data this way.
Challenge: Plot Line Width by Attribute
In the example above, we set the line widths to be 1, 2, 3, and 4. Because R orders factor levels alphabetically by default, this gave us a plot where woods roads (the last factor level) were the thickest and boardwalks were the thinnest.
Let’s create another plot where we show the different line types with the following thicknesses:
- woods road size = 6
- boardwalks size = 1
- footpath size = 3
- stone wall size = 2
First we need to look at the levels of our factor to see what order the road types are in:
We then can create our
line_widthvector setting each of the levels to the desired thickness.
line_width <- c(1, 3, 2, 6)
Now we can create our plot.
ggplot() + geom_sf(data = lines_HARV, aes(size = TYPE)) + scale_size_manual(values = line_width) + ggtitle("NEON Harvard Forest Field Site", subtitle = "Roads & Trails - Line width varies") + coord_sf()
Add Plot Legend
We can add a legend to our plot too. When we add a legend, we use the following elements to specify labels and colors:
bottomright: We specify the location of our legend by using a default keyword. We could also use
levels(objectName$attributeName): Label the legend elements using the categories of levels in an attribute (e.g., levels(lines_HARV$TYPE) means use the levels boardwalk, footpath, etc).
fill =: apply unique colors to the boxes in our legend.
palette()is the default set of colors that R applies to all plots.
Let’s add a legend to our plot. We will use the
that we created above to color the legend. We can customize the
appearance of our legend by manually setting different parameters.
ggplot() + geom_sf(data = lines_HARV, aes(color = TYPE), size = 1.5) + scale_color_manual(values = road_colors) + labs(color = 'Road Type') + ggtitle("NEON Harvard Forest Field Site", subtitle = "Roads & Trails - Default Legend") + coord_sf()
We can change the appearance of our legend by manually setting different parameters.
legend.text: change the font size
legend.box.background: add an outline box
ggplot() + geom_sf(data = lines_HARV, aes(color = TYPE), size = 1.5) + scale_color_manual(values = road_colors) + labs(color = 'Road Type') + theme(legend.text = element_text(size = 20), legend.box.background = element_rect(size = 1)) + ggtitle("NEON Harvard Forest Field Site", subtitle = "Roads & Trails - Modified Legend") + coord_sf()
new_colors <- c("springgreen", "blue", "magenta", "orange") ggplot() + geom_sf(data = lines_HARV, aes(color = TYPE), size = 1.5) + scale_color_manual(values = new_colors) + labs(color = 'Road Type') + theme(legend.text = element_text(size = 20), legend.box.background = element_rect(size = 1)) + ggtitle("NEON Harvard Forest Field Site", subtitle = "Roads & Trails - Pretty Colors") + coord_sf()
You can modify the default R color palette using the palette method. For example
palette(terrain.colors(6)). You can reset the palette colors using
Challenge: Plot Lines by Attribute
Create a plot that emphasizes only roads where bicycles and horses are allowed. To emphasize this, make the lines where bicycles are not allowed THINNER than the roads where bicycles are allowed. NOTE: this attribute information is located in the
Be sure to add a title and legend to your map. You might consider a color palette that has all bike/horse-friendly roads displayed in a bright color. All other lines can be black.
First we need to make sure that the
BicyclesHoattribute is a factor and check how many levels it has.
Next, we will create a new object
lines_removeNAthat removes missing values.
lines_removeNA <- lines_HARV[!is.na(lines_HARV$BicyclesHo),]
In our plot, we will set colors so that only the allowed roads are magenta, and we will set line width so that the first factor level is thicker than the others.
# First, create a data frame with only those roads where bicycles and horses are allowed lines_showHarv <- lines_removeNA %>% filter(BicyclesHo == "Bicycles and Horses Allowed") # Next, visualise using ggplot ggplot() + geom_sf(data = lines_HARV) + geom_sf(data = lines_showHarv, aes(color = BicyclesHo), size = 2) + scale_color_manual(values = "magenta") + ggtitle("NEON Harvard Forest Field Site", subtitle = "Roads Where Bikes and Horses Are Allowed") + coord_sf()
Challenge: Plot Polygon by Attribute
- Create a map of the state boundaries in the United States using the data located in your downloaded data folder:
NEON-DS-Site-Layout-Files/US-Boundary-Layers\US-State-Boundaries-Census-2014. Apply a fill color to each state using its
regionvalue. Add a legend.
First we read in the data and check how many levels there are in the
state_boundary_US <- st_read("data/NEON-DS-Site-Layout-Files/US-Boundary-Layers/US-State-Boundaries-Census-2014.shp")
Reading layer `US-State-Boundaries-Census-2014' from data source `/home/travis/build/datacarpentry/r-raster-vector-geospatial/_episodes_rmd/data/NEON-DS-Site-Layout-Files/US-Boundary-Layers/US-State-Boundaries-Census-2014.shp' using driver `ESRI Shapefile' Simple feature collection with 58 features and 10 fields geometry type: MULTIPOLYGON dimension: XYZ bbox: xmin: -124.7258 ymin: 24.49813 xmax: -66.9499 ymax: 49.38436 z_range: zmin: 0 zmax: 0 CRS: 4326
Next we set a color vector with that many items:
colors <- c("purple", "springgreen", "yellow", "brown", "navy")
Now we can create our plot:
ggplot() + geom_sf(data = state_boundary_US, aes(color = region), size = 1) + scale_color_manual(values = colors) + ggtitle("Contiguous U.S. State Boundaries") + coord_sf()
Spatial objects in
sfare similar to standard data frames and can be manipulated using the same functions.
Almost any feature of a plot can be customized using the various functions and options in the