Basic Visualization and Plotting with glatos
Overview
Teaching: 30 min
Exercises: 0 minQuestions
How can I use glatos to plot my data?
What kinds of plots can I make with my data?
Objectives
Now that we’ve cleaned and processed our data, we can use glatos’ built-in plotting tools to make quick and effective visualizations out of it. One of the simplest visualizations is an abacus plot to display animal detections against the appropriate stations. To this end, glatos supplies a built-in, customizable abacus_plot function.
# Visualizing Data - Abacus Plots ####
# ?glatos::abacus_plot
# customizable version of the standard VUE-derived abacus plots
abacus_plot(detections_w_events,
location_col='station',
main='NSBS Detections by Station') # can use plot() variables here, they get passed thru to plot()
This is good, but you can see that the plot is cluttered. Rather than plotting our entire dataset, let’s try filtering out a single animal ID and only plotting that. We can do this right in our call to abacus_plot with the filtering syntax we’ve previously covered.
# pick a single fish to plot
abacus_plot(detections_filtered[detections_filtered$animal_id== "NSBS-Xena",],
location_col='station',
main="NSBS-Xena Detections By Station")
Other plots are available in glatos and can show different facets of our data. If we want to see the physical distribution of our stations, for example, a bubble plot will serve us better.
# Bubble Plots for Spatial Distribution of Fish ####
# bubble variable gets the summary data that was created to make the plot
detections_filtered
?detection_bubble_plot
# We'll use raster to get a polygon to plot against
library(geodata)
library(geodata)
CAN <- geodata::gadm("CANADA", level=1, path=".")
NS <- CAN[CAN$NAME_1=="Nova Scotia",]
bubble_station <- detection_bubble_plot(detections_filtered,
background_ylim = c(43.4, 46),
background_xlim = c(-66, -62),
map = NS,
location_col = 'station',
out_file = 'nsbs_bubbles_by_stations.png')
bubble_station
bubble_array <- detection_bubble_plot(detections_filtered,
background_ylim = c(43.4, 46),
background_xlim = c(-66, -62),
map = NS,
out_file = 'nsbs_bubbles_by_array.png')
bubble_array
These examples provide just a brief introduction to some of the plotting available in glatos.
Key Points