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01-raster-structure.md

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+---
+title: Plot Multiple Vector Layers
+teaching: 40
+exercises: 20
+source: Rmd
+---
+
+
+```{.warning}
+Warning in
+download.file("https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip",
+: cannot open URL
+'https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip':
+HTTP status was '500 Internal Server Error'
+```
+
+```{.error}
+Error in download.file("https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip", : cannot open URL 'https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip'
+```
+
+::::::::::::::::::::::::::::::::::::::: objectives
+
+- Plot multiple vector layers in the same plot.
+- Apply custom symbols to spatial objects in a plot.
+- Create a multi-layered plot with raster and vector data.
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+:::::::::::::::::::::::::::::::::::::::: questions
+
+- How can I create map compositions with custom legends using ggplot?
+- How can I plot raster and vector data together?
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+
+
+
+
+::::::::::::::::::::::::::::::::::::::::::  prereq
+
+## 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 builds upon
+[the previous episode](07-vector-shapefile-attributes-in-r/)
+to work with vector layers in R and explore how to plot multiple
+vector layers. It also covers how to plot raster and vector data together on the
+same plot.
+
+## Load the Data
+
+To work with vector data in R, we can use the `sf` library. The `terra`
+package also allows us to explore metadata using similar commands for both
+raster and vector files. Make sure that you have these packages loaded.
+
+We will continue to work with the three ESRI `shapefile` that we loaded in the
+[Open and Plot Vector Layers in R](06-vector-open-shapefile-in-r/) episode.
+
+## Plotting Multiple Vector Layers
+
+In the [previous episode](07-vector-shapefile-attributes-in-r/), we learned how
+to plot information from a single vector layer and do some plot customization
+including adding a custom legend. However, what if we want to create a more
+complex plot with many vector layers and unique symbols that need to be
+represented clearly in a legend?
+
+Now, let's create a plot that combines our tower location (`point_HARV`), site
+boundary (`aoi_boundary_HARV`) and roads (`lines_HARV`) spatial objects. We
+will need to build a custom legend as well.
+
+To begin, we will create a plot with the site boundary as the first layer. Then
+layer the tower location and road data on top using `+`.
+
+
+```r
+ggplot() +
+  geom_sf(data = aoi_boundary_HARV, fill = "grey", color = "grey") +
+  geom_sf(data = lines_HARV, aes(color = TYPE), size = 1) +
+  geom_sf(data = point_HARV) +
+  ggtitle("NEON Harvard Forest Field Site") +
+  coord_sf()
+```
+
+<img src="fig/08-vector-plot-shapefiles-custom-legend-rendered-plot-many-shapefiles-1.png" style="display: block; margin: auto;" />
+
+Next, let's build a custom legend using the symbology (the colors and symbols)
+that we used to create the plot above. For example, it might be good if the
+lines were symbolized as lines. In the previous episode, you may have noticed
+that the default legend behavior for `geom_sf` is to draw a 'patch' for each
+legend entry. If you want the legend to draw lines or points, you need to add
+an instruction to the `geom_sf` call - in this case, `show.legend = 'line'`.
+
+
+```r
+ggplot() +
+  geom_sf(data = aoi_boundary_HARV, fill = "grey", color = "grey") +
+  geom_sf(data = lines_HARV, aes(color = TYPE),
+          show.legend = "line", size = 1) +
+  geom_sf(data = point_HARV, aes(fill = Sub_Type), color = "black") +
+  scale_color_manual(values = road_colors) +
+  scale_fill_manual(values = "black") +
+  ggtitle("NEON Harvard Forest Field Site") +
+  coord_sf()
+```
+
+<img src="fig/08-vector-plot-shapefiles-custom-legend-rendered-plot-custom-shape-1.png" style="display: block; margin: auto;" />
+
+Now lets adjust the legend titles by passing a `name` to the respective `color`
+and `fill` palettes.
+
+
+```r
+ggplot() +
+  geom_sf(data = aoi_boundary_HARV, fill = "grey", color = "grey") +
+  geom_sf(data = point_HARV, aes(fill = Sub_Type)) +
+  geom_sf(data = lines_HARV, aes(color = TYPE), show.legend = "line",
+          size = 1) +
+  scale_color_manual(values = road_colors, name = "Line Type") +
+  scale_fill_manual(values = "black", name = "Tower Location") +
+  ggtitle("NEON Harvard Forest Field Site") +
+  coord_sf()
+```
+
+<img src="fig/08-vector-plot-shapefiles-custom-legend-rendered-create-custom-legend-1.png" style="display: block; margin: auto;" />
+
+Finally, it might be better if the points were symbolized as a symbol. We can
+customize this using `shape` parameters in our call to `geom_sf`: 16 is a point
+symbol, 15 is a box.
+
+:::::::::::::::::::::::::::::::::::::::::  callout
+
+## Data Tip
+
+To view a short list of `shape` symbols,
+type `?pch` into the R console.
+
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+
+```r
+ggplot() +
+  geom_sf(data = aoi_boundary_HARV, fill = "grey", color = "grey") +
+  geom_sf(data = point_HARV, aes(fill = Sub_Type), shape = 15) +
+  geom_sf(data = lines_HARV, aes(color = TYPE),
+          show.legend = "line", size = 1) +
+  scale_color_manual(values = road_colors, name = "Line Type") +
+  scale_fill_manual(values = "black", name = "Tower Location") +
+  ggtitle("NEON Harvard Forest Field Site") +
+  coord_sf()
+```
+
+<img src="fig/08-vector-plot-shapefiles-custom-legend-rendered-custom-symbols-1.png" style="display: block; margin: auto;" />
+
+:::::::::::::::::::::::::::::::::::::::  challenge
+
+## Challenge: Plot Polygon by Attribute
+
+1. Using the `NEON-DS-Site-Layout-Files/HARV/PlotLocations_HARV.shp` ESRI `shapefile`,
+  create a map of study plot locations, with each point colored by the soil
+  type (`soilTypeOr`). How many different soil types are there at this
+  particular field site? Overlay this layer on top of the `lines_HARV` layer
+  (the roads). Create a custom legend that applies line symbols to lines and
+  point symbols to the points.
+
+2. Modify the plot above. Tell R to plot each point, using a different symbol
+   of `shape` value.
+
+:::::::::::::::  solution
+
+## Answers
+
+First we need to read in the data and see how many unique soils are represented
+in the `soilTypeOr` attribute.
+
+
+```r
+plot_locations <-
+  st_read("data/NEON-DS-Site-Layout-Files/HARV/PlotLocations_HARV.shp")
+```
+
+```{.output}
+Reading layer `PlotLocations_HARV' from data source 
+  `/home/runner/work/r-raster-vector-geospatial/r-raster-vector-geospatial/site/built/data/NEON-DS-Site-Layout-Files/HARV/PlotLocations_HARV.shp' 
+  using driver `ESRI Shapefile'
+Simple feature collection with 21 features and 25 fields
+Geometry type: POINT
+Dimension:     XY
+Bounding box:  xmin: 731405.3 ymin: 4712845 xmax: 732275.3 ymax: 4713846
+Projected CRS: WGS 84 / UTM zone 18N
+```
+
+```r
+plot_locations$soilTypeOr <- as.factor(plot_locations$soilTypeOr)
+levels(plot_locations$soilTypeOr)
+```
+
+```{.output}
+[1] "Histosols"   "Inceptisols"
+```
+
+Next we can create a new color palette with one color for each soil type.
+
+
+```r
+blue_orange <- c("cornflowerblue", "darkorange")
+```
+
+Finally, we will create our plot.
+
+
+```r
+ggplot() +
+  geom_sf(data = lines_HARV, aes(color = TYPE), show.legend = "line") +
+  geom_sf(data = plot_locations, aes(fill = soilTypeOr),
+          shape = 21, show.legend = 'point') +
+  scale_color_manual(name = "Line Type", values = road_colors,
+     guide = guide_legend(override.aes = list(linetype = "solid",
+                                              shape = NA))) +
+  scale_fill_manual(name = "Soil Type", values = blue_orange,
+     guide = guide_legend(override.aes = list(linetype = "blank", shape = 21,
+                                              colour = NA))) +
+  ggtitle("NEON Harvard Forest Field Site") +
+  coord_sf()
+```
+
+<img src="fig/08-vector-plot-shapefiles-custom-legend-rendered-harv-plot-locations-bg-1.png" style="display: block; margin: auto;" />
+
+If we want each soil to be shown with a different symbol, we can give multiple
+values to the `scale_shape_manual()` argument.
+
+
+```r
+ggplot() +
+  geom_sf(data = lines_HARV, aes(color = TYPE), show.legend = "line", size = 1) +
+  geom_sf(data = plot_locations, aes(fill = soilTypeOr, shape = soilTypeOr),
+          show.legend = 'point', size = 3) +
+  scale_shape_manual(name = "Soil Type", values = c(21, 22)) +
+  scale_color_manual(name = "Line Type", values = road_colors,
+     guide = guide_legend(override.aes = list(linetype = "solid", shape = NA))) +
+  scale_fill_manual(name = "Soil Type", values = blue_orange,
+     guide = guide_legend(override.aes = list(linetype = "blank", shape = c(21, 22),
+     color = blue_orange))) +
+  ggtitle("NEON Harvard Forest Field Site") +
+  coord_sf()
+```
+
+<img src="fig/08-vector-plot-shapefiles-custom-legend-rendered-harv-plot-locations-pch-1.png" style="display: block; margin: auto;" />
+
+:::::::::::::::::::::::::
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+:::::::::::::::::::::::::::::::::::::::  challenge
+
+## Challenge: Plot Raster \& Vector Data Together
+
+You can plot vector data layered on top of raster data using the `+` to add a
+layer in `ggplot`. Create a plot that uses the NEON AOI Canopy Height Model
+`data/NEON-DS-Airborne-Remote-Sensing/HARV/CHM/HARV_chmCrop.tif` as a base
+layer. On top of the CHM, please add:
+
+- The study site AOI.
+- Roads.
+- The tower location.
+
+Be sure to give your plot a meaningful title.
+
+:::::::::::::::  solution
+
+## Answers
+
+
+```r
+ggplot() +
+  geom_raster(data = CHM_HARV_df, aes(x = x, y = y, fill = HARV_chmCrop)) +
+  geom_sf(data = lines_HARV, color = "black") +
+  geom_sf(data = aoi_boundary_HARV, color = "grey20", size = 1) +
+  geom_sf(data = point_HARV, pch = 8) +
+  ggtitle("NEON Harvard Forest Field Site w/ Canopy Height Model") +
+  coord_sf()
+```
+
+<img src="fig/08-vector-plot-shapefiles-custom-legend-rendered-challenge-vector-raster-overlay-1.png" style="display: block; margin: auto;" />
+
+:::::::::::::::::::::::::
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+
+
+:::::::::::::::::::::::::::::::::::::::: keypoints
+
+- Use the `+` operator to add multiple layers to a ggplot.
+- Multi-layered plots can combine raster and vector datasets.
+- Use the `show.legend` argument to set legend symbol types.
+- Use the `scale_fill_manual()` function to set legend colors.
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+