sas gplot slides 1 26 2011
TRANSCRIPT
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SAS: Proc GPLOT
Computing for Research I
01/26/2011N. Baker
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Introduction to SAS/GRAPH
•
Graphics component of SAS system.
•
Includes charts, plots, and maps in both 2 and 3 dimensions.
•
Procedures included GCHART, GPLOT, GMAP, GCONTOUR etc…
•
We will focus on PROC GPLOT
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What can be done with SAS/GRAPH?
These samples courtesy of Robert Allison’s SAS Graph Examples
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Elements of SAS/GRAPH Overview
Taken from SAS 9.2 documentation
ODS
Destination
Elements
Global Statements
Procedure Step
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Elements of SAS/GRAPH PROC GPLOT: Specifying an input data set
Similar to all other SAS PROC’s–
Proc gplot
data=<libname>.<data set><options>;
Options include setting annotate data sets, image mapping for drill-down plots in web applications, Creating Uniform axis across plots, and specifying SAS catalog for placement of output.
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Elements of SAS/GRAPH PROC GPLOT: Plotting
•
You can use up to 2 plots statements at a time, however, at least one Plot statement is required.
•
The plot statement is used to control the axis, plotting points, labels, tick marks, and the plot legend.
•
The only required arguments are…–
Plot <Y Variable>*<X Variable> / <options>;
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Elements of SAS/GRAPH PROC GPLOT: Plotting Options
•
Options for plotting –
Plot options
•
Legend= or nolegend: specifies figure legend options•
Overlay: allows overlay of more than one Y variable•
Skipmiss: breaks the plotting line where Y values are missing
–
Appearance option•
Axis: Specifies axis label and value options•
Symbol: Specified symbol options•
href, vref: Draws vertical or horizontal reference lines on plot•
frame/fr
or noframe/nofr: specifies whether or not to frame the plot
•
caxis/ca, cframe/cfr, chref/ch, cvref/cv, ctext/c: specifies colors used for axis, frame, text or reference lines.
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Introduction to SAS/GRAPH
•
We will begin with rather simple code and let SAS decide how our graph will look.
•
Then we will step through a few options that allow us to control and adjust the graphic output.
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Examples 2 Variable Plotting / Scatter plots
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Examples 2 Variables
•
Suppose subjects are given a doses of experimental medication based on body weight over a 24 hour period (mg/24hrs). Variable X
•
On the following day, each subject had their Vascular Cell Adhesion Molecule (μg/ml)
levels
measured. Variable Y1
•
The investigators are interested in seeing a plot of the dose given vs. the plasma VCAM levels to see if there may be an effect of the drug dose.
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Examples 2 Variables
y1
0
1
2
3
x
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9
Very basic plot, below we get all of the default options. Not very exciting. Definitely not publication quality.
Cannot read axis marks
Axis labels don’t describe the data
Crowded Axis
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Examples 2 Variables: AXIS Statements
•
AXIS<1..99> <options>;–
Label Option;
•
Angle/a=degrees (0-359)•
Color/c=text color
•
Font/f=font •
Height/h=text height (default=1)
•
Justify=(left/center/right)•
Label=“text string”
–
Options precede label
•
axis1 label=(a=90 c=black f=“arial”
h=1.2 “time” a=90 c=black f=“arial”
h=1.0 “hours”);
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Examples 2 Variables: AXIS Statements
•
AXIS<1..99> <options>;–
Order Option
•
Order=(a to b by c): major tick marks will show up at intervals based on c.
–
Example order=(0 to 3 by 1);
–
Value Option•
value=(“”
“”
“”): applies text label to each major tick.
–
Example Value=( “Start”
“Middle”
“End”)
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Examples 2 Variables: AXIS Statements
Resets previous options
Horizontal axis
(X Variable)
Vertical axis
(Y Variable)
Call Axis statements
NOTE: you can also place the AXIS statements within the gplot
proc
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Examples 2 Variables: AXIS Statements
Plas
ma
Leve
l
0
1
2
3
D o s em g /2 4 H rs
0.0 0 .1 0 .2 0 .3 0.4 0 .5 0 .6 0 .7 0 .8 0 .9 1.0 1 .1 1 .2 1 .3 1 .4 1 .5 1.6 1.7 1 .8 1 .9
The LABEL options helped make the axis labels meaningful, but the axis tick marks remain crowded
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Examples 2 Variables: AXIS Statement
Added ORDER
option to Axis statement
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Examples 2 Variables: AXIS Statement
Plas
ma
Leve
l
0
1
2
3
D o sem g/24 H rs
0.0 0.5 1.0 1.5 2.0
The axis are less crowded, but still very hard to read, using the Value= option will help.
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Examples 2 Variables: AXIS Statement
Added VALUE option to Axis
statement
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Examples 2 Variables
Plas
ma
Leve
l
0.0
1.0
2.0
3.0
D o sem g /24 H rs
0 .0 0 .5 1 .0 1 .5 2 .0
Now about those data points!
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Examples 2 Variables: Symbol Statement
•
Symbol<1…255> <options>;–
Symbol options
•
Color= value color•
Ci=line color
•
Height=symbol height•
Line=line
type
•
Value=symbol•
Width=thickness factor
•
Interpol=point interpolations
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Examples 2 Variables: Symbol Statement
•
Symbol<1…255> <options>;–
Symbol options
•
Interpolation options–
Join, box, hilo
interpolation, regression, spline, standard deviations.
•
value options–
Dot, circle, star, square, plus, minus, “text value”.
•
Color options–
256 colors available,
www.devenezia.com/docs/SAS/sas-colors.html
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Examples 2 Variables: Symbol Statement
Symbol options•
Interpolation options
–
None–
Join: points connected by straight line–
Needle: vertical line from horizontal axis to point–
Stepx: (L,R,C) step function, stepxJ
will add a verticle
line to each step plot
–
stdkxxx: (M,P,J,B,T) k=1,2,3 (standard deviations) or »
stdM=SEM, stdp=uses pooled sample variance, stdj=joins the errors, T will give tops and bottoms to error lines, where B will request error bars.
–
HILOxxx: (T,B,C,J)
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Examples 2 Variables: Symbol Statement
Symbol options•
Interpolation options
–
R-series interpolation–
Rxxxxxxx»
RL: linear regression»
RQ: Quadratic Regression»
RC: Cubic Regression»
CLM: CI for mean predicted values»
CLI: CI for Individual predicted values»
90, 95, 99: confidence limits
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Examples 2 Variables: SYMBOL Statement
Plas
ma
Leve
l
0.0
1.0
2.0
3.0
D o s em g /2 4 H r s
0 .0 0 .5 1 .0 1 .5 2 .0
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Examples 2 Variables: Adding Regression Lines
Plas
ma
Leve
l
0.0
1.0
2.0
3.0
D o s em g /2 4 H r s
0 .0 0 .5 1 .0 1 .5 2 .0
R e g re s s io n E q u a t io n : y 1 = 0 . 4 8 1 1 7 3 + 1 . 2 6 9 4 3 3 * x
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Examples Grouping Variables
•
Many times we want to look at group differences.
•
Demographic groups, treatment groups, etc…
•
Grouping variable must be in the data file.
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Examples Grouping Variables
You need to add a new SYMBOL statement for the each additional group.
Add the grouping variable to the PLOT statement
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Examples Grouping Variables
Plas
ma
Leve
l
0.0
1.0
2.0
3.0
D osem g/24 Hrs
0.0 0.5 1.0 1.5 2.0
gender Fem ale M ale
Not bad, but the figure legend is not well placed.
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Examples Grouping Variables: Legend Statement
•
Legend<1…99> <options>;–
Legend options
•
Across=: number of columns •
Down=: number of rows
•
Frame/noframe•
Position=(bottom, middle, top) (left, center, right)
(inside, outside)•
Origin=(x,y)
•
Label=•
Order=
•
Value=
These options are the same as within the axis statement discussed earlier
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Examples Grouping Variables: Legend Statement
Legend Statement
Call Legend Statement
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Examples Grouping Variables: Legend Statement
Plas
ma
Leve
l
0.0
1.0
2.0
3.0
D o sem g/24 H rs
0.0 0 .5 1 .0 1 .5 2 .0
G ender Fem aleM ale
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Examples Repeated Measures/Longitudinal Plotting
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Examples Repeated Measures/Longitudinal Plotting
•
Suppose that you have many observations on each subject taken at various time points.
•
40 subjects•
2 treatments (Placebo and Active med)
•
5 time points (baseline plus 4 1-week intervals)–
During the last week, both treatment groups receive Placebo•
Data should be in the Long format
At diagnosis, subjects are randomized to an experimental treatment or placebo. During the final week of treatment, all subjects will receive active medicatio.
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Examples Repeated Measures/Longitudinal Plotting
Create appropriate axis and legend statements as before.AXIS for X (time) variable
AXIS for Y (Response) variable
Added TITLE statement for plot
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Examples Repeated Measures/Longitudinal Plotting
Res
pons
e
0
1 0
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
1 0 0
T im e S in c e D ia g n o s is : W e e k s
B a s e lin e 1 2 3 4
In d i v i d u a l D i s e a s e P r o g r e s s i o n
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Examples Repeated Measures/Longitudinal PlottingJoins the dots,
By ID
Res
pons
e
0
1 0
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
1 0 0
T im e S in c e D ia g n o s is : W e e k s
B a s e lin e 1 2 3 4
In d i v i d u a l D i s e a s e P r o g r e s s i o n
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Examples Repeated Measures/Longitudinal Plotting
Res
pons
e
0
1 0
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
1 0 0
T im e S in c e D ia g n o s is : W e e k s
B a s e lin e 1 2 3 4
In d i v i d u a l D i s e a s e P r o g r e s s i o nT re a tm e n t G ro u p Tr e a tm a n t A P la c e b o
Plot data by trt
group and create a symbol statement for each group
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Examples Using the Overlay statement to stack plots
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Examples Overlay 2 plots w/ the same data
Suppose that you are asked to graphically show progression of tumor growth for a group of subjects and overlay the progression of each treatment group.
50 subjects randomized to either low or high dose medication.
Tumor size is measured at baseline as well as the following 9 weeks.
The investigator would like an easy to present plot containing both pieces of information for a presentation to his peers.
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Examples Overlay 2 plots w/ the same data
Tum
or G
row
th
0
10
20
30
40
50
60
70
80
Time Since Diagnosis: W eeks
Baseline 1 2 3 4 5 6 7 8 9
Individual Disease Progression
Tum
or G
row
th
0
10
20
30
40
50
60
70
80
T im e S ince D iagnosis : W eeks
Baseline 1 2 3 4 5 6 7 8 9
Individual D isease ProgressionT reatment G roup Low Dose High Dose
Plot of individual values as before
Plot of treatment group means and Standard errors as before
Grouping variable Symbol repeats
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Examples Overlay 2 plots w/ the same data
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Examples Overlay 2 plots w/ the same data
Tum
or G
row
th
0
10
20
30
40
50
60
70
80
Time Since Randomization: W eeks
Baseline 1 2 3 4 5 6 7 8 9
0
10
20
30
40
50
60
70
80
Individual Disease ProgressionTreatment Group Low Dose High Dose
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Examples Overlay multiple plots from different variables
Use proc logistic to output the predicted probability of developing nephropathy given the baseline Oxidized LDL immune complex level
as well as the 95% confidence limits.
Many PROCs
can output predicted values, adjusted means, along with point wise confidence values.
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Examples Overlay multiple plots from different variables
Prob
. of N
ephr
opat
hy (9
5% C
I)
0.0
0.2
0.4
0.6
0.8
Baseline Ox LDL-IC
1.80 2.14 2.48 2.82 3.16 3.50 3.84 4.18 4.52 4.86 5.20 5.54 5.88 6.22 6.56 6.90
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Examples Overlay multiple plots from different variables
Bas
elin
e LD
L &
HD
L (m
g/dl
)
0
50
100
150
200
250
Baseline OxLDL-IC Quartile1st 2nd 3rd 4th
Baseline O
xLDL-IC
0
100
200
300
400
500Baseline Characteristics OxLDL-IC LDL Cholesterol
HDL CholesterolBaseline Characteristics OxLDL-IC
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Examples Overlay multiple plots from different variables
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The Annotate Facility
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The Annotate Facility Introduction
The Annotate Facility allows SAS users to customize graphicaloutput. The customizations can be data driven or user specified. Text, shapes, lines and images can be added to output graphics
Step 1. Create an annotate data setthis data file will give commands to SAS/GRAPH Specific variables must be in the annotate data set. Others are
allowed but ignored
What, how, and where are defined by these variables.Table 1 list important variables.
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The Annotate Facility Introduction
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The Annotate Facility Introduction
The Annotate FUNCTION variable tells SAS what to do
The annotate coordinate system allows for flexibility in placing objects within the output. There are 12 possible conditions.
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The Annotate Facility Introduction
Taken from Mink and Pasta, SUGI 31
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The Annotate Facility Introduction
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The Annotate FacilityH
bA1c
6 .0 %
6.5 %
7.0 %
7.5 %
8.0 %
8.5 %
9.0 %
9.5 %
10.0 %
S tu d y T im eY e ars
B L 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9
M e a n H bA 1 c % durr ing D C C T /E D IC s tudy
Proc GPLOT global options help make graphs more pleasing, however, there are cases where more work is needed to fully explain the data
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The Annotate Facility
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The Annotate Facility
Created shaded regions to designate study sections
Deleted regions of non interest
Added treatment group and study section labels
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The Annotate Facility
$ 0.00
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$ 0.90
$ 1.00
YearJan. 2007 Jan. 2008 Jan. 2009 Jan. 2010 Jan. 2011
Individual Net WorthAs a Function of Original Worth
BORING!Suppose you want To jazz up your plots for a Presentation. You can place a pictureOr graphic behind you data to accent The results. We are going to place an image behind the data, but only below The data series. NEAT!
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The Annotate Facility
Anno data set 1:Will place the image of the dollar over the plotting area.
Anno data set 2:Will create whiteSpace above the Plotted line over time.
SET the anno data sets and call them in the GPLOT statement
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The Annotate Facility
$ 0.00
$ 0.10
$ 0.20
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$ 0.40
$ 0.50
$ 0.60
$ 0.70
$ 0.80
$ 0.90
$ 1.00
YearJan. 2007 Jan. 2008 Jan. 2009 Jan. 2010 Jan. 2011
Individual Net WorthAs a Function of Original Worth
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The End