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Stata: Kaplan-Meir曲線

Stataの特徴は比較的簡単に美しいグラフの作成できることです。Stataのサンプルデータdrug2を使って、Kaplan-Meier曲線(白黒)を作成してみましょう。

use https://www.stata-press.com/data/r16/drug2
sts graph, by(drug)

このKaplan-Meier曲線に設定を追加して、下図を作成します。

この図を作成するためには、以下の魔法を唱える必要があります。

sts graph, xsize(3.7) ysize(3.7) by(drug) failure    ytitle("Cumulative probability of incidence of outcome" " ", size(small))  ylabel(0.0(0.2)1, angle(0) labsize(small) format(%9.1f) nogrid)  ytick(0.0(0.1)0.6)    xtitle(" " "Observational period (year)", size(small))  xlabel(0 "0" 12 "1" 24 "2" 36 "3" 48 "4", labsize(small))  xtick(0(6)48)   title("A", size("medlarge") span position(11))    plot1opt(lpattern(dash)) plot2opt(lpattern(solid)) plotopt(lcolor(black))    legend(ring(0) position(5) cols(1) region(lcolor(white)) order(1 "Non-user (n=20)" 2 "User (n=28)") size(small) title("Drug use", size("small") color("black")))    risktable(0(12)48, size(small) order(1 "Non-user" 2 "User") rowtitle(, justification(left)) title(, size(small)))    text(1 48 "P<0.001", placement(sw) size(small))    graphregion(color(white) lcolor(white))

それでは、この魔法が作られた過程を確認していきましょう。

グラフのサイズを変更する

A4サイズ(8.27 × 11.69インチ)に2 x 3個のグラフが収まるサイズにしたいので、図のサイズを3.7 × 3.7 インチに設定します。

sts graph, xsize(3.7) ysize(3.7)
sts graph, xsize(3.7) ysize(3.7)

カテゴリ別の累積アウトカム発症率を算出する

Y軸を、累積生存率ではなく、累積アウトカム発症率に変更し、durgカテゴリ別のKaplan-Meier曲線を描きます。

sts graph, xsize(3.7) ysize(3.7) by(drug) failure
sts graph, xsize(3.7) ysize(3.7) by(drug) failure

Y軸を調整する

Y軸名(ytitle)を”Cumulative probability of incidence of outcome”にします。デフォルトの文字サイズは大きいので、小さくします(small)。デフォルト設定のままだと軸と軸名がくっつきすぎるので、Y軸名に空白行を1行挿入して、軸と軸名の間隔を少し広げます。

Y軸の数値(ylabel)の向き(angle)を水平にして、その間隔を0.2にしますが、目盛り線(tick)の間隔は0.1にします。ラベルの文字を少し小さくして(small)、小数点1桁表示にします。ガイド線(グリッド)を消します。

sts graph, xsize(3.7) ysize(3.7) by(drug) failure    ytitle("Cumulative probability of incidence of outcome" " ", size(small))  ylabel(0.0(0.2)1, angle(0) labsize(small) format(%9.1f) nogrid)  ytick(0.0(0.1)0.6)
sts graph, xsize(3.7) ysize(3.7) by(drug) failure ytitle(“Cumulative probability of incidence of outcome” ” “, size(small)) ylabel(0.0(0.2)1, angle(0) labsize(small) format(%9.1f) nogrid) ytick(0.0(0.1)0.6)

X軸を調整する

X軸名(xtitle)を”Observational period (year)”にします。デフォルトの文字サイズは大きいので、小さくします(small)。デフォルト設定のままだと軸と軸名がくっつきすぎるので、X軸名に空白行を1行挿入して、軸と軸名の間隔を少し広げます。

追跡期間データの単位は月(0〜48)ですが、X軸の単位を年に変換するために、第0, 12, 24, 36, 48月に0, 1, 2, 3, 4を表示させます。目盛り線(tick)の間隔を6ヶ月にします。ラベルの文字を少し小さくします(small)。

sts graph, xsize(3.7) ysize(3.7) by(drug) failure    ytitle("Cumulative probability of incidence of outcome" " ", size(small))  ylabel(0.0(0.2)1, angle(0) labsize(small) format(%9.1f) nogrid)  ytick(0.0(0.1)0.6)    xtitle(" " "Observational period (year)", size(small))  xlabel(0 "0" 12 "1" 24 "2" 36 "3" 48 "4", labsize(small))  xtick(0(6)48)
sts graph, xsize(3.7) ysize(3.7) by(drug) failure ytitle(“Cumulative probability of incidence of outcome” ” “, size(small)) ylabel(0.0(0.2)1, angle(0) labsize(small) format(%9.1f) nogrid) ytick(0.0(0.1)0.6) xtitle(” ” “Observational period (year)”, size(small)) xlabel(0 “0” 12 “1” 24 “2” 36 “3” 48 “4”, labsize(small)) xtick(0(6)48)

タイトルを変更する

グラフのタイトル”A”を、グラフ全体の左上にやや大きめ(medlarge)で追加します。

sts graph, xsize(3.7) ysize(3.7) by(drug) failure    ytitle("Cumulative probability of incidence of outcome" " ", size(small))  ylabel(0.0(0.2)1, angle(0) labsize(small) format(%9.1f) nogrid)  ytick(0.0(0.1)0.6)    xtitle(" " "Observational period (year)", size(small))  xlabel(0 "0" 12 "1" 24 "2" 36 "3" 48 "4", labsize(small))  xtick(0(6)48)   title("A", size("medlarge") span position(11))    
sts graph, xsize(3.7) ysize(3.7) by(drug) failure ytitle(“Cumulative probability of incidence of outcome” ” “, size(small)) ylabel(0.0(0.2)1, angle(0) labsize(small) format(%9.1f) nogrid) ytick(0.0(0.1)0.6) xtitle(” ” “Observational period (year)”, size(small)) xlabel(0 “0” 12 “1” 24 “2” 36 “3” 48 “4”, labsize(small)) xtick(0(6)48) title(“A”, size(“medlarge”) span position(11))

生存曲線のレイアウトを変更する

drugカテゴリ別の生存曲線のレイアウトを変更します。カラーイラストは論文掲載料が追加されることが多いので、生存曲線の色を黒に統一して、drug=0を点線、drug=1を実線に設定します。

sts graph, xsize(3.7) ysize(3.7) by(drug) failure ytitle("Cumulative probability of incidence of outcome" " ", size(small)) ylabel(0.0(0.2)1, angle(0) labsize(small) format(%9.1f) nogrid) ytick(0.0(0.1)0.6) xtitle(" " "Observational period (year)", size(small)) xlabel(0 "0" 12 "1" 24 "2" 36 "3" 48 "4", labsize(small)) xtick(0(6)48) title("A", size("medlarge") span position(11)) plot1opt(lpattern(dash)) plot2opt(lpattern(solid)) plotopt(lcolor(black))
sts graph, xsize(3.7) ysize(3.7) by(drug) failure ytitle(“Cumulative probability of incidence of outcome” ” “, size(small)) ylabel(0.0(0.2)1, angle(0) labsize(small) format(%9.1f) nogrid) ytick(0.0(0.1)0.6) xtitle(” ” “Observational period (year)”, size(small)) xlabel(0 “0” 12 “1” 24 “2” 36 “3” 48 “4”, labsize(small)) xtick(0(6)48) title(“A”, size(“medlarge”) span position(11)) plot1opt(lpattern(dash)) plot2opt(lpattern(solid)) plotopt(lcolor(black))

凡例を修正する

凡例を、生存曲線のプロット領域内(ring(0))の右下(5時方向)に、縦1列(cols(1))で表示する。枠線を白に設定して見えなくする(region(lcolor(white)))。カテゴリ名を”Drug use”にして、drugカテゴリ0には”Non-user (n=20)”を、drugカテゴリ1には”User (n=28)”を、黒文字で小さめに表示する。

sts graph, xsize(3.7) ysize(3.7) by(drug) failure    ytitle("Cumulative probability of incidence of outcome" " ", size(small))  ylabel(0.0(0.2)1, angle(0) labsize(small) format(%9.1f) nogrid)  ytick(0.0(0.1)0.6)    xtitle(" " "Observational period (year)", size(small))  xlabel(0 "0" 12 "1" 24 "2" 36 "3" 48 "4", labsize(small))  xtick(0(6)48)   title("A", size("medlarge") span position(11))    plot1opt(lpattern(dash)) plot2opt(lpattern(solid)) plotopt(lcolor(black))    legend(ring(0) position(5) cols(1) region(lcolor(white)) order(1 "Non-user (n=20)" 2 "User (n=28)") size(small) title("Drug use", size("small") color("black")))
sts graph, xsize(3.7) ysize(3.7) by(drug) failure ytitle(“Cumulative probability of incidence of outcome” ” “, size(small)) ylabel(0.0(0.2)1, angle(0) labsize(small) format(%9.1f) nogrid) ytick(0.0(0.1)0.6) xtitle(” ” “Observational period (year)”, size(small)) xlabel(0 “0” 12 “1” 24 “2” 36 “3” 48 “4”, labsize(small)) xtick(0(6)48) title(“A”, size(“medlarge”) span position(11)) plot1opt(lpattern(dash)) plot2opt(lpattern(solid)) plotopt(lcolor(black)) legend(ring(0) position(5) cols(1) region(lcolor(white)) order(1 “Non-user (n=20)” 2 “User (n=28)”) size(small) title(“Drug use”, size(“small”) color(“black”)))

Number at riskを追加する

Number at riskを12ヶ月毎に追加する。drugカテゴリ名は小さめ(small)に左揃えで”Non-user”と”User”と表示する。

sts graph, xsize(3.7) ysize(3.7) by(drug) failure    ytitle("Cumulative probability of incidence of outcome" " ", size(small))  ylabel(0.0(0.2)1, angle(0) labsize(small) format(%9.1f) nogrid)  ytick(0.0(0.1)0.6)    xtitle(" " "Observational period (year)", size(small))  xlabel(0 "0" 12 "1" 24 "2" 36 "3" 48 "4", labsize(small))  xtick(0(6)48)   title("A", size("medlarge") span position(11))    plot1opt(lpattern(dash)) plot2opt(lpattern(solid)) plotopt(lcolor(black))    legend(ring(0) position(5) cols(1) region(lcolor(white)) order(1 "Non-user (n=20)" 2 "User (n=28)") size(small) title("Drug use", size("small") color("black")))    risktable(0(12)48, size(small) order(1 "Non-user" 2 "User") rowtitle(, justification(left)) title(, size(small)))
sts graph, xsize(3.7) ysize(3.7) by(drug) failure ytitle(“Cumulative probability of incidence of outcome” ” “, size(small)) ylabel(0.0(0.2)1, angle(0) labsize(small) format(%9.1f) nogrid) ytick(0.0(0.1)0.6) xtitle(” ” “Observational period (year)”, size(small)) xlabel(0 “0” 12 “1” 24 “2” 36 “3” 48 “4”, labsize(small)) xtick(0(6)48) title(“A”, size(“medlarge”) span position(11)) plot1opt(lpattern(dash)) plot2opt(lpattern(solid)) plotopt(lcolor(black)) legend(ring(0) position(5) cols(1) region(lcolor(white)) order(1 “Non-user (n=20)” 2 “User (n=28)”) size(small) title(“Drug use”, size(“small”) color(“black”))) risktable(0(12)48, size(small) order(1 “Non-user” 2 “User”) rowtitle(, justification(left)) title(, size(small)))

テキスト(P値)を追加する

XY座標(1, 48)の左下(sw = southwest)にテキスト”P<0.001″を追加する。

sts graph, xsize(3.7) ysize(3.7) by(drug) failure    ytitle("Cumulative probability of incidence of outcome" " ", size(small))  ylabel(0.0(0.2)1, angle(0) labsize(small) format(%9.1f) nogrid)  ytick(0.0(0.1)0.6)    xtitle(" " "Observational period (year)", size(small))  xlabel(0 "0" 12 "1" 24 "2" 36 "3" 48 "4", labsize(small))  xtick(0(6)48)   title("A", size("medlarge") span position(11))    plot1opt(lpattern(dash)) plot2opt(lpattern(solid)) plotopt(lcolor(black))    legend(ring(0) position(5) cols(1) region(lcolor(white)) order(1 "Non-user (n=20)" 2 "User (n=28)") size(small) title("Drug use", size("small") color("black")))    risktable(0(12)48, size(small) order(1 "Non-user" 2 "User") rowtitle(, justification(left)) title(, size(small)))    text(1 48 "P<0.001", placement(sw) size(small))
sts graph, xsize(3.7) ysize(3.7) by(drug) failure ytitle(“Cumulative probability of incidence of outcome” ” “, size(small)) ylabel(0.0(0.2)1, angle(0) labsize(small) format(%9.1f) nogrid) ytick(0.0(0.1)0.6) xtitle(” ” “Observational period (year)”, size(small)) xlabel(0 “0” 12 “1” 24 “2” 36 “3” 48 “4”, labsize(small)) xtick(0(6)48) title(“A”, size(“medlarge”) span position(11)) plot1opt(lpattern(dash)) plot2opt(lpattern(solid)) plotopt(lcolor(black)) legend(ring(0) position(5) cols(1) region(lcolor(white)) order(1 “Non-user (n=20)” 2 “User (n=28)”) size(small) title(“Drug use”, size(“small”) color(“black”))) risktable(0(12)48, size(small) order(1 “Non-user” 2 “User”) rowtitle(, justification(left)) title(, size(small))) text(1 48 “P<0.001”, placement(sw) size(small))

テキストの配置(placement)には、sw以外にも下記を設定できます。テキストの表示位置に応じて適宜変更して下さい。

  • c = centered on the point, vertically and horizontally
  • n = above the point, centered
  • ne = above and to the right of the point
  • e = right of the point, vertically centered
  • se = below and to the right of the point
  • s = below point, centered
  • sw = below and to the left of the point
  • w = left of the point, vertically centered
  • nw = above and to the left of the point

Stata公式マニュアル https://www.stata.com/manuals/g-3added_text_options.pdf

背景色を変更する

グラフ領域の背景を白色に設定して完成!

sts graph, xsize(3.7) ysize(3.7) by(drug) failure    ytitle("Cumulative probability of incidence of outcome" " ", size(small))  ylabel(0.0(0.2)1, angle(0) labsize(small) format(%9.1f) nogrid)  ytick(0.0(0.1)0.6)    xtitle(" " "Observational period (year)", size(small))  xlabel(0 "0" 12 "1" 24 "2" 36 "3" 48 "4", labsize(small))  xtick(0(6)48)   title("A", size("medlarge") span position(11))    plot1opt(lpattern(dash)) plot2opt(lpattern(solid)) plotopt(lcolor(black))    legend(ring(0) position(5) cols(1) region(lcolor(white)) order(1 "Non-user (n=20)" 2 "User (n=28)") size(small) title("Drug use", size("small") color("black")))    risktable(0(12)48, size(small) order(1 "Non-user" 2 "User") rowtitle(, justification(left)) title(, size(small)))    text(1 48 "P<0.001", placement(sw) size(small))    graphregion(color(white) lcolor(white))