Computing for Research ISpring 2012

Primary Instructor: Elizabeth Garrett-Mayer

Stata GraphicsFebruary 16

Basic syntax for commands• prefix: command varlist, options

• Examples:– regress y x, level(90)– by race: sum y x, detail– ttest y, by(x) unequal

Stata Graphics

• Maybe we can just end class now! • Check out these links:

– http://www.ats.ucla.edu/stat/stata/library/GraphExamples/default.htm

– http://www.ats.ucla.edu/stat/stata/topics/graphics.htm

– http://data.princeton.edu/stata/graphics.html– http://www.stata.com/capabilities/graphics.html

Basic univariate displays

• Boxplots• Stem and leaf• Histograms• Density plots

Ceramide Data

• Let’s look at the ceramide markers• What are their distributions?• Are there outliers?• Should we consider taking logs, or using % change?

Results of a phase II trial of gemcitabine plus doxorubicin in patients with recurrent head and neck cancers: serum C₁₈-ceramide as a novel biomarker for monitoring response.Saddoughi SA, Garrett-Mayer E, Chaudhary U, O'Brien PE, Afrin LB, Day TA, Gillespie MB, Sharma AK, Wilhoit CS, Bostick R, Senkal CE, Hannun YA, Bielawski J, Simon GR, Shirai K, Ogretmen B. Clin Cancer Res. 2011 Sep 15;17(18):6097-105. Epub 2011 Jul 26.

Histogram

• hist c180

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0 20 40 60C18 ceramide

Let’s make it prettier

* prettier histogramshist c18 , freq xaxis(1 2) ylabel(0(2)24) xlabel(20 "Twenty" 40 "Forty")

hist c18, title("Histogram of C18 Ceramide") subtitle("PI: K. Shirai")

hist c18, ytitle("number of patients") freq yline(0(10)20)

hist c18, xaxis(1 2) xlabel(19.6 "mean" 11.9 "median", axis(2) grid)

finding help on these can sometimes be tricky! e.g. help axis_choice_options

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PI: K. ShiraiHistogram of C18 Ceramide

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Boxplots

• graph box c180

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Boxplotsgraph box c18, by(cycle)graph box c18, over(cycle)

tab cyclegraph box c18 if cycle<7, over(cycle)

sort patient cyclemerge m:1 patient using "Ptdata.GemDox.dta"graph box c18 if cycle<7, over(cycle) over(gender)

graph hbox c18, over(initial) capsize(5)

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Graphs by Cycle

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graph hbox c18, over(initial) capsize(5)

graph hbox c18, over(initial) medtype(marker)medmarker(msymbol(+) msize(large))

graph hbox c18, over(initial) ytitle(“C18”)

Labels

• Sometimes xlabels cannot be applied (e.g. boxplots)

• need to label your values• Example: cycle for boxplots

– label define cycle 1 "cycle 1" 3 "cycle 3" 5 "cycle 5" 7 "cycle 7"

– label values cycle cycle– graph box c18 if cycle<7, over(cycle)

• (Hint: use this on the homework!)

Stem and Leaf. stem c18

Stem-and-leaf plot for c18ceramide (C18 ceramide)

c18ceramide rounded to nearest multiple of .1plot in units of .1

0** | 42,43,44,46 0** | 57,57,67,81,89,90,96,98,99,99 1** | 01,06,08,08,14,15,19,20,35,44 1** | 62 2** | 03,15,16,18,19,19,22 2** | 82 3** | 17 3** | 4** | 23,49 4** | 58,68,68 5** | 5** | 6** | 37 6** | 86

Dotplot

• Excellent way to show data across groups when you have a relatively small dataset

• dotplot y, over(group)

dotplot c18, over(cycle)dotplot c18, over(gender)dotplot c18, over(gender) nogroupdotplot c18, over(gender) nogroup jitter(3)dotplot c18, over(gender) nogroup median center

Dotplot, by gender

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Scatterplots• Two way graph• Syntax:

– graph twoway scatter y x1 x2– graph twoway scatter y x1

• Example:– graph twoway scatter c18 totalceramide

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Regression example

• Scatterplot• Residual plots• Leverage • Fitted line with raw data

Code graph twoway scatter c18 totalcerregress c18 totalcer

* residual plot* (residual vs. fitted)rvfplot

* the long way* 1. generate a new variable from the regression, residualspredict resid, res* 2. generate a new variable from the regression, fitted valuespredict fitscatter res fit, yline(0)* leverage vs. residual plotlvr2plot

* take transform of C18?gladder c18boxcox c18

* generate new variablegen logc18=log(c18)scatter logc18 totalcerscatter logc18 totalcer, mlabel(gender) scatter logc18 totalcer, mlabel(gender)

s(i)scatter logc18 totalcer, s(Oh)

* redo regressionregress logc18 totalcerrvfplot, yline(0)lvr2plotpredict logfit

* make plot of fitted model and raw datascatter logfit logc18 totalcerscatter logfit logc18 totalcer, s(i o) c(l .)graph twoway scatter logfit totalcer, s(i) c(l) || scatter logc18 totalcer, s(o) c(.)

The next graph to create

Fancier way to put regression linesinfile str14 country setting effort change /// using http://data.princeton.edu/wws509/datasets/effort.raw

graph twoway scatter change setting graph twoway (scatter change setting ) (lfit change setting )graph twoway (scatter change setting ) (qfit change setting )graph twoway (scatter change setting ) (lfitci change setting )

• scatter makes a scatterplot of the two variables

• lfit plots the regression line of y on x

• qfit plots a fitted quadratic model of y on x

• lfitci plots the line AND a confidence interval!

Fancier way to put regression lines0

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change Fitted values

Plot using qfit

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Plot using lfitci

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• One slight problem with the labels is the overlap of Costa Rica and Trinidad Tobago (and to a lesser extent Panama and Nicaragua).

• We can solve this problem by specifying the position of the label relative to the marker using a 12-hour clock (so 12 is above, 3 is to the right, 6 is below and 9 is to the left) and the mlabv() option.

• We create a variable to hold the position set by default to 3 o'clock and then move Costa Rica to 9 o'clock and Trinidad Tobago to just a bit above that at 11 o'clock (we can also move Nicaragua and Panama up a bit, say to 2 o'clock).

graph twoway (lfitci change setting) (scatter change setting, mlabel(country) )

gen pos=3 replace pos = 11 if country == "TrinidadTobago" replace pos = 9 if country == "CostaRica" replace pos = 2 if country == "Panama" | country == "Nicaragua“

graph twoway (lfitci change setting) /// (scatter change setting, mlabel(country) mlabv(pos) )

Bolivia

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Legends

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Fertility Decline by Social Setting

Bolivia

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Fertility Decline by Social Setting

graph twoway (lfitci change setting) /// (scatter change setting, mlabel(country) mlabv(pos) ) /// , title("Fertility Decline by Social Setting") /// ytitle("Fertility Decline") /// legend(ring(0) pos(5) order(2 "linear fit" 1 "95% CI"))

graph twoway (lfitci change setting) /// (scatter change setting, mlabel(country) mlabv(pos) ) /// , title("Fertility Decline by Social Setting") /// ytitle("Fertility Decline") /// legend(off)

Spaghetti plotsCommand available from UCLA: spagplot

* spaghetti plotsclear insheet using "I:\MUSC Oncology\Shirai, Keisuke\October2010\ceramide.csv"findit spagplotspagplot c18 cycle, id(patient)spagplot c18 cycle, id(patient) nofit

* remove patients who only have cycle=1sort patient cycle by patient: gen visit=_negen maxvis=max(visit), by(patient)spagplot c18 cycle if maxvis>1, id(patient) nofit

* or, use c(L)graph twoway scatter c18 cycle if maxvis>1, c(L)help connectstyle

other neat stuff

• graph matrix• saving graphs: click and save as desired format• saving and combining (see princeton site,

section 3.3)– http://data.princeton.edu/stata/graphics.html

• See GraphExamples on ucla site:– http://www.ats.ucla.edu/stat/stata/library/GraphExamples/