We will use the tidyverse a lot this semester. It is a suite of packages that handles plotting and data wrangling efficiently.
You only have to install the library once. You have to load it using the library() function each time you start an R session.
#install.packages("tidyverse")library(tidyverse)
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.2 ✔ readr 2.1.4
✔ forcats 1.0.0 ✔ stringr 1.5.0
✔ ggplot2 3.4.2 ✔ tibble 3.2.1
✔ lubridate 1.9.2 ✔ tidyr 1.3.0
✔ purrr 1.0.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
1.2 Reading data
The following lines will read in the data we will use for this exercise. Don’t worry about this right now beyond running it, we will talk more about it later.
Pine <-read_csv("PINE_Jan-Mar_2010.csv")
Rows: 2160 Columns: 8
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (2): StationID, surrogate
dbl (5): cfs, year, quarter, month, day
dttm (1): datetime
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
SNP <-read_csv("PINE_NFDR_Jan-Mar_2010.csv")
Rows: 4320 Columns: 8
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (2): StationID, surrogate
dbl (5): cfs, year, quarter, month, day
dttm (1): datetime
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
RBI <-read_csv("Flashy_Dat_Subset.csv")
Rows: 49 Columns: 26
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (4): STANAME, STATE, CLASS, AGGECOREGION
dbl (22): site_no, RBI, RBIrank, DRAIN_SQKM, HUC02, LAT_GAGE, LNG_GAGE, PPTA...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Basic ggplot syntax
1.3 Our first ggplot
Let’s look at the Pine data, plotting streamflow (the cfs column) by the date (datetime column). We will show the time series as a line.
ggplot(data = Pine, aes(x = datetime, y = cfs))+geom_line()
1.4 Change point type
Now let’s make the same plot but show the data as points, using the pch parameter in geom_point() we can change the point type to any of the following:
pch options from R help file
ggplot(data = Pine, aes(x = datetime, y = cfs))+geom_point(pch =8)
1.5 Set colors
We can also “easily” change the color. Easily is in quotes because this often trips people up. If you put color = “blue” in the aesthetic function, think about what that is telling ggplot. It says “control the color using”blue”“. That doesn’t make a whole lot of sense, so neither does the output… Try it.
What happens is that if color = “blue” is in the aesthetic, you are telling R that the color used in the geom represents “blue”. This is very useful if you have multiple geoms in your plot, are coloring them differently, and are building a legend. But if you are just trying to color the points, it kind of feels like R is trolling you… doesn’t it?
Take the color = “blue” out of the aesthetic and you’re golden.
ggplot(data = Pine, aes(datetime, y = cfs, color ="blue"))+geom_point()
ggplot(data = Pine, aes(x = datetime, y = cfs))+geom_point(color ="blue")
1.6 Controlling color with a third variable and other functions
Let’s plot the data as a line again, but play with it a bit.
First: make the line blue
Second: change the theme
Third: change the axis labels
Fourth: color by discharge
ggplot(data = Pine, aes(x = datetime, y = cfs, color = cfs))+geom_line()+ylab("Discharge (cfs)")+xlab(element_blank())+theme_classic()
1.7 Plotting multiple groups
The SNP dataset has two different streams: Pine and NFDR
We can look at the two of those a couple of different ways
First, make two lines, colored by the stream by adding color = to your aesthetic.
You must tell the facet_wrap what variable to use to make the separate panels (facet =). It’ll decide how to orient them or you can tell it how. We want them to be on top of each other so we are going to tell it we want 2 rows by setting nrow = 2. Note that we have to put the column used to make the facets in quotes after facets =
You can also use facet_grid() to break your plots up into panels based on two variables. Below we will create a panel for each month in each watershed. Adding scales = “free” allows facet_grid to change the axes. By default, all axes will be the same. This is often what we want, so we can more easily compare magnitudes, but sometimes we are looking for patterns more, so we may want to let the axes have whatever range works for the individual plots.
We can look at these data in other ways as well. A very useful way to look at the variation of two groups is to use a boxplot.
Because the data span several orders of magnitude, we will have to log the y axis to see the differences between the two streams. We do that by adding scale_y_log10()
ggplot(data = SNP, aes(x = StationID, y = cfs)) +stat_boxplot()+scale_y_log10()
1.11 More about color, size, etc
Let’s play around a bit with controlling color, point size, etc with other data.
We can control the size of points by putting size = in the aes() and color by putting color =
If you use a point type that has a background, like #21, you can also set the background color using bg =
If points are too close together to see them all you can use a hollow point type or set the alpha lower so the points are transparent (alpha = )
Finally: You can add multiple geoms to the same plot. Examples of when you might want to do this are when you are showing a line fit and want to show the points as well, or maybe showing a boxplot and want to show the data behind it. You simply add additional geom_… lines to add additional geoms.
ggplot(RBI, aes(RBI, DRAIN_SQKM, color = AGGECOREGION))+stat_smooth(method ="lm", linetype =2)+geom_point()
