如何建立定序區域圖

如何建立定序區域圖

我該如何創建這個乳膠中?我對 Latex 比較陌生,沒有創建任何圖表的經驗。

數字和文字本身是任意的,只要有空間即可。我還在尋找陰影“條形圖”以具有適當的縮放比例,例如綠色部分的起點(點313)應該是左側條形總寬度的313/1139。請注意,這些數字應該能夠被任何一組數字取代。同樣的想法適用於帶箭頭的行。總寬度為textwidth。

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答案1

歡迎來到 TeX.SX!

你可以使用 TikZ繪製你的圖表。我強烈建議閱讀該包的文檔了解如何使用它。例如,您可以這樣開始:

\documentclass[border=1mm, tikz]{standalone}

\newcounter{rowstart}
\newcounter{rowend}

\newcounter{sequencestart}
\newcounter{sequenceend}

\newcounter{matchrevstart}
\newcounter{matchrevend}

\newcounter{matchfwdstart}
\newcounter{matchfwdend}

\newcommand{\drawsequence}{%
\begin{tikzpicture}[x=.25mm, y=5cm, 
        row/.append style={black},
        sequence/.append style={row, fill=green},
    ]

\coordinate (rstart) at (\therowstart,0);
\coordinate (sstart) at (\thesequencestart,0);
\coordinate (send) at (\thesequenceend,0);
\coordinate (rend) at (\therowend,0);

\draw[row] ([yshift=5mm]rstart) rectangle coordinate[pos=.5] (xrleft) ([yshift=-5mm]sstart);
\draw[sequence] ([yshift=5mm]sstart) rectangle coordinate[pos=.5] (xsequence) ([yshift=-5mm]send);
\draw[row] ([yshift=5mm]send) rectangle coordinate[pos=.5] (xrright) ([yshift=-5mm]rend);

\node at ([yshift=7.5mm]rstart) {\therowstart};
\node at ([yshift=7.5mm]sstart) {\thesequencestart};
\node at ([yshift=7.5mm]send) {\thesequenceend};
\node at ([yshift=7.5mm]rend) {\therowend};

\node at (xrleft) {5' UTR};
\node at (xrright) {3' UTR};
\node at (xsequence) {Protein Coding Sequence};

\draw[dashed] ([yshift=-5mm]\thematchrevstart,0) -- ++(0,-.8);
\draw[dashed] ([yshift=-5mm]\thematchfwdend,0) -- ++(0,-.8);

\draw[->] (\thematchrevstart,-.25) node[above right] {\thematchrevstart} -- node[above, pos=.5] {\footnotesize Region of exact match, Reverse strand sequencing} (\thematchrevend,-.25) node[above left] {\thematchrevend};

\draw[<-] (\thematchfwdstart,-.5) node[above right] {\thematchfwdstart} -- node[above, pos=.5] {\footnotesize Region of exact match, Forward strand sequencing} (\thematchfwdend,-.5) node[above left] {\thematchfwdend};

\draw[<->] (\thematchrevstart,-.75) -- node[above, pos=.5] {\footnotesize Extent of cloned cDNA, excluding the polyA tail} (\thematchfwdend,-.75);

\end{tikzpicture}%
}

\begin{document}

\setcounter{rowstart}{1}
\setcounter{rowend}{1139}

\setcounter{sequencestart}{313}
\setcounter{sequenceend}{765}

\setcounter{matchrevstart}{213}
\setcounter{matchrevend}{1001}

\setcounter{matchfwdstart}{429}
\setcounter{matchfwdend}{1039}

\drawsequence

\end{document}

結果如下:

在此輸入影像描述


但是,您說過,結果應該與文本一樣寬。因此,我對上面的程式碼做了一些調整,以便結果始終縮放到文字寬度。我必須稍微增加箭頭的間距,因為文字不適合。

\documentclass{article}
\usepackage{tikz}

\newcounter{rowstart}
\newcounter{rowend}

\newcounter{sequencestart}
\newcounter{sequenceend}

\newcounter{matchrevstart}
\newcounter{matchrevend}

\newcounter{matchfwdstart}
\newcounter{matchfwdend}

\newcommand{\drawsequence}{%
\noindent\begin{tikzpicture}[
        row/.append style={black},
        sequence/.append style={row, fill=green},
    ]

\coordinate (rstart) at ({\therowstart/\therowend*\textwidth},0);
\coordinate (sstart) at ({\thesequencestart/\therowend*\textwidth},0);
\coordinate (send) at ({\thesequenceend/\therowend*\textwidth},0);
\coordinate (rend) at ({\therowend/\therowend*\textwidth},0);

\coordinate (mrstart) at ({\thematchrevstart/\therowend*\textwidth},0);
\coordinate (mfstart) at ({\thematchfwdstart/\therowend*\textwidth},0);
\coordinate (mrend) at ({\thematchrevend/\therowend*\textwidth},0);
\coordinate (mfend) at ({\thematchfwdend/\therowend*\textwidth},0);

\draw[row] ([yshift=2.5mm]rstart) rectangle coordinate[pos=.5] (xrleft) ([yshift=-2.5mm]sstart);
\draw[sequence] ([yshift=2.5mm]sstart) rectangle coordinate[pos=.5] (xsequence) ([yshift=-2.5mm]send);
\draw[row] ([yshift=2.5mm]send) rectangle coordinate[pos=.5] (xrright) ([yshift=-2.5mm]rend);

\node[anchor=west] at ([yshift=5mm]rstart) {\therowstart};
\node at ([yshift=5mm]sstart) {\thesequencestart};
\node at ([yshift=5mm]send) {\thesequenceend};
\node[anchor=east] at ([yshift=5mm]rend) {\therowend};

\node at (xrleft) {5' UTR};
\node at (xrright) {3' UTR};
\node at (xsequence) {Protein Coding Sequence};

\draw[dashed] ([yshift=-2.5mm]mrstart) -- ([yshift=-36mm]mrstart);
\draw[dashed] ([yshift=-2.5mm]mfend) -- ([yshift=-36mm]mfend);

\draw[->] ([yshift=-15mm]mrstart) node[above right] {\thematchrevstart} -- node[above, pos=.5, text width=50mm, align=center] {\footnotesize Region of exact match, Reverse strand sequencing} ([yshift=-15mm]mrend) node[above left] {\thematchrevend};

\draw[<-] ([yshift=-25mm]mfstart) node[above right] {\thematchfwdstart} -- node[above, pos=.5, text width=50mm, align=center] {\footnotesize Region of exact match, Forward strand sequencing} ([yshift=-25mm]mfend) node[above left] {\thematchfwdend};

\draw[<->] ([yshift=-35mm]mrstart) -- node[above, pos=.5, text width=50mm, align=center] {\footnotesize Extent of cloned cDNA, excluding the polyA tail} ([yshift=-35mm]mfend);

\end{tikzpicture}%
}

\begin{document}

\setcounter{rowstart}{1}
\setcounter{rowend}{1139}

\setcounter{sequencestart}{313}
\setcounter{sequenceend}{765}

\setcounter{matchrevstart}{213}
\setcounter{matchrevend}{1001}

\setcounter{matchfwdstart}{429}
\setcounter{matchfwdend}{1039}

\drawsequence

\end{document}

結果:

在此輸入影像描述

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