This course covers the essential exploratory techniques for summarizing data. These techniques are typically applied before formal modeling commences and can help inform the development of more complex statistical models. Exploratory techniques are also important for eliminating or sharpening potential hypotheses about the world that can be addressed by the data. We will cover in detail the plotting systems in R as well as some of the basic principles of constructing data graphics. We will also cover some of the common multivariate statistical techniques used to visualize high-dimensional data.
Base Plotting System (part 2)
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Del curso dictado por Johns Hopkins University
Exploratory Data Analysis
4013 calificaciones
De la lección
Week 1
This week covers the basics of analytic graphics and the base plotting system in R. We've also included some background material to help you install R if you haven't done so already.
Conoce a los instructores
Roger D. Peng, PhDAssociate Professor, Biostatistics
Bloomberg School of Public Health
Jeff Leek, PhDAssociate Professor, Biostatistics
Bloomberg School of Public Health
Brian Caffo, PhDProfessor, Biostatistics
Bloomberg School of Public Health
So some of the key base plotting functions that you'll use a lot of
course is the, one, the first is the plot function which makes a scatterplot.
And it can make other types of
plots depending on whether you're, you're plotting a
special type of object, but for the
most part you usually want to make scatterplots.
Uh,lines is a, is a function that doesn't create a plot but it adds to a plot
and so sometimes you want to connect a lot of dots together so you want to make like
uh,a time series type of font.
You want to make, you want to draw
lines instead of scatterplot lines is useful for that.
points, adds points to a plot, so sometimes
you want to create a plot, and then you want to
add some other points that might represent a
different group or a different subset of the population.
Text as labels, so you want to annotate the plot with text labels.
Title adds so text can be used, I should say, to add labels within the plot.
And the title function is typically used to add annotations outside the
plot, like x and y axis labels, titles, subtitles, and things like that.
Mtext is, the m stands for margins, so it's
used to place text in the margins of the plot,
both the inner and the outer margin, and the
axis function is for use for specifying the axis ticks.
So here is a couple, a couple examples of how to
make plots, and then adding, annotating them, here I am plotting
the wind and ozone that I had before.
Or scatterplot, but now I'm adding a title to the top of the plot.
So here is the ozone and wind from, in New York City.
In this plot, I'm again doing a
scatterplot, but I, instead of using the title
function to add the title, I just, I put the title directly into the call
to plot, but then, what I want to do is, I want to sub-set, I want to kind of
plot all of the data points that are in the month of May a different color.
And so what I do is I subset
the data frame just to include the observations from
month equals 5, and then I use the points function to add, to kind of re add points,
but this time color them blue.
So you can see in the plot below that the the, they're a subset of
blue points, and those correspond to the, to the data points in the month of May.
Now I could do um,um, more subsets so I can plot them different colors.
Cause here I'm, I'm plotting but the um,the initializing a plot but
then one thing you can see is I added the argument type equals
n and so what type equals n means it basically sets up
the plot and initializes the graphics
device but it doesn't actually plot anything.
So it doesn't put anything into the plotting region.
It just
makes a, it sets up all the other stuff in the plot without the actual data.
And then as I, in order to put the data into
the plot, I kind of go through subsets of the data frame.
To add the data from the month of May, and add data for the month of not May.
So, for the month of May, I make that color blue, and then, for
the other months that are not equal to May, I just make that color red.
So, you can see all of the other points are red.
So now, I can kind of accurately see which ones are blue, which ones are
May, without kind of ov, over plotting existing points.
And then as a last touch, I add a legend to the top right part of the plot, so I
can distinguish, which ones are May, which ones are not May.
Finally, one common thing you will typically want
to do is add a regression line or
a smoother to a plot, so here I've
just added a regression line to this same scatterplot.
So I first make
the scatterplot and you notice, I changed the default.
Plotting character pch to be 20.
So, 20 is a kind of small filled in circle.
And then I fit a linear model to the data, which is using the LM function.
And then I just call the abline function, which
is another annotation function, ah,and I just pass it,
the linear model object and I specify lwd equals
to 2, which is a thicker line than the
typical default line.
So abline can interpret the regression model output and
plot a line, plot with a given intercept and slope.
And so here you can see, I've added the regression line to the plot.
Um,and so you can see,and you can see the downward trend.
So, all the previous plots into the single plot
that you might, that would appear on the graphics device.
But sometimes you want to have multiple plots on a single device.
So here I made two plots. One plot is ozone versus wind.
And the other one plot is ozone versus solar radiation using the same data set.
And so in order to do that I can just
set the par mfrow equals to one row and two columns.
So I They, I can make the two plots side by side.
And then I just call plot twice.
So every time I call plot, it creates a new plot.
And so the first one will be, the in the kind of left hand side and
the second column plot will be in the
right hand side and that's how I use mfrow.
Now, you can see that, when I use multiple plots, some I have a title
on each plot so that it tells me kind of what the two variables are.
And the first one's ozone and wind, second one's ozone and solar
radiation, and the third one here is ozone and temperature.
But sometimes you want to have a label that's.
Kind of covering the entire panel of plots.
So that's what the outer margin is for.
So here in this call of the par I set mfrow equal to one row, three columns.
I set the margins to be a little bit
smaller than defaults and then I set the outer
margin to be actually bigger than default, the b,
the default for the outer margin is zero all around.
So on the top I want a little extra space so I can add the title.
Ozone and weather in New York City, which is
kind of a title for the entire panel of plots.
And then I call plot three times to make the three plots and then
I use mtext to add the kind of outer title to this panel of plots.
So that was a quick, kind of introduction to the base
plotting system, covers some of the basic functions that you would use,
that you would use including plot and
a couple of annotation functions like, A line.
And points and things like that.
So, it's, you can see that by creating.
And when you create base plots, you are kind
of building up a plot by function by function.
And you kind of end up with a, with many live code to create one plot.
And that's kind of that's how, that's typical of lots of base plots.
Every plots starts with a function that initiates
the plot, so like, plot or hist or box plot, and then a series
of functions which will typically annotate the
plot by adding points, lines, text and legends.
So the, the base plotting system is very flexible.
It, it gives you a lot of control over all of the various details of the plot.
Of course this can be a little bit tedious if you need
to control everything all the time but often the defaults are okay.
And but, the flexibility is quite useful if
you want to make, kind of, publication quality plots.
and, and, and so, it's nice to have that de-, that degree
of control, with all, for things like legends, spacing's and all that.
And so, so that's the, kind of the base plotting system.
We'll talk more about the other plotting systems in other lectures.
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