Cfrgtkky

I am trying to recreate this diagram from a paper for my thesis. The idea would be that I can scale it to different sizes, only use parts of it and insert different nodes like the circles and triangles.

I have tried reproducing it, but I am quite unexperienced with tikz, so after hours of desperatly trying to make it work I have come up with a huge, unelegant solution, that doesn't really look the way I want it to.

PassOptionsToPackage{svgnames}{xcolor}

documentclass[12pt,a4paper]{scrartcl}

usepackage{tikz, pgf}

usepackage{xltxtra}

renewcommand{familydefault}{sfdefault}

usepackage[T1]{fontenc}

usetikzlibrary{

positioning,

shapes.geometric,

shapes.misc,

calc,

fit,

matrix}



begin{document}

begin{tikzpicture} [pics/myHexagon/.style args={#1/#2/#3}%

{

    code=

    {

     pgfmathsetmacro{mySqrt}{sqrt(3)/2}

    defr{#1}

    defa{#2}

    defc{#3}

    draw [cm={r,0,.5*r,mySqrt*r,(0,0)},fill=c,text=white] 

    (1+a,0) coordinate (-corner 0) coordinate (-corner 6) 

    -- (a,1) coordinate (-corner 1)

    -- (-1-a,1) coordinate (-corner 2)

    -- (-1-a,0) coordinate (-corner 3)

    -- (-a,-1)  coordinate (-corner 4)

    -- (1+a,-1) coordinate (-corner 5)

    -- cycle;

    {asfd}

}

}]



    draw   (0,0)   pic {myHexagon={.6/.3/RoyalBlue}};

    draw  (2,0)    pic {myHexagon={.6/.3/DarkMagenta}};

    draw  (4,0)    pic {myHexagon={.6/.3/RoyalBlue}};

    draw  (6,0)    pic {myHexagon={.6/.3/DarkMagenta}};





    draw  (2,-1.5) node [shape=ellipse,draw,minimum height=1cm,fill=red] {L-Ala};

    draw  (1,-3)   node [shape=ellipse,draw,minimum height=1cm, fill=yellow] {D-Glu};

    draw  (0,-4.5) node [shape=ellipse,draw,minimum height=1cm] {L-Lys};

    draw  (0,-6)   node [shape=ellipse,draw,minimum height=1cm] {D-Ala};



    draw  (1.7,-4.5)   node [shape=circle,draw,minimum height=.75cm] {Gly};

    draw  (3,-4.5) node [shape=circle,draw,minimum height=.75cm] {Gly};

    draw  (4.3,-4.5)   node [shape=circle,draw,minimum height=.75cm] {Gly};

    draw  (5.6,-4.5)   node [shape=circle,draw,minimum height=.75cm] {Gly};

    draw  (6.9,-4.5)   node [shape=circle,draw,minimum height=.75cm] {Gly};



    draw  (8.5,-4.5)   node [shape=ellipse,draw,minimum height=1cm] {D-Ala};

    draw  (7.5,-6) node [shape=ellipse,draw,minimum height=1cm] {L-Lys};

    draw  (6.5,-7.5)   node [shape=ellipse,draw,minimum height=1cm] {D-Glu};

    draw  (5.5,-9) node [shape=ellipse,draw,minimum height=1cm] {L-Ala};



    draw   (3.5,-10.5) pic {myHexagon={.6/.3/RoyalBlue}};

    draw  (1.5,-10.5)  pic {myHexagon={.6/.3/DarkMagenta}};

    draw  (7.5,-10.5)  pic {myHexagon={.6/.3/RoyalBlue}};

    draw  (5.5,-10.5)  pic {myHexagon={.6/.3/DarkMagenta}};

end{tikzpicture}







end{document}

Could someone please help me simplify and complete it?
Thanks!

[edit]

I should mention that I used Scaling only a portion of a TikZ polygon for the polygons.

I would like to suggest using a chamfered rectangle for the hexagon, and set a large value of for chamfered rectangle xsep. The pgfmanual writes on p. 736

Sets the distance that the chamfer extends horizontally beyond the
node contents (which includes the inner sep). If ⟨length⟩ is large,
such that the top and bottom chamfered edges would cross, then
⟨length⟩ is ignored and the chamfered edges are drawn so that they
meet in the middle.

and shows a hexagon. Further, you are loading positioning, and I would like to suggest using it for relative positioning. (You may also look into chains, but I personally I find this sometimes a bit of an overkill.) So here is a first proposal.

PassOptionsToPackage{svgnames}{xcolor}

documentclass[12pt,a4paper]{scrartcl}

usepackage{tikz, pgf}

usepackage{xltxtra}

renewcommand{familydefault}{sfdefault}

usepackage[T1]{fontenc}

usetikzlibrary{

positioning,

shapes.geometric,

shapes.misc,

shadows.blur,

calc}

newcounter{hexa}

begin{document}

begin{tikzpicture}[my hexa/.style={blur shadow,chamfered rectangle,chamfered rectangle

xsep=2cm,draw,text=white,path picture={%

draw[white] let p1=($(path picture bounding box.north)-(path picture

bounding box.east)$) in

([xshift=-1pt]path picture bounding box.east)

-- ++(-y1+1pt,y1-1pt) -- ++(2*x1,0);}},

my elli/.style={blur shadow,ellipse,draw,text=white,path picture={%

fill[white] let p1=($(path picture bounding box.north)-(path picture

bounding box.east)$) in ([xshift=-1pt]path picture bounding box.east)

to[out=90,in=0,looseness=0.8] ([yshift=-1pt]path picture bounding box.north)

to[out=0,in=90,looseness=0.7] cycle;

}},

shaded triangle/.style={blur shadow,regular polygon,regular polygon sides=3,shape border rotate=0,

inner sep=1pt,draw,inner color=#1!10,outer color=#1}]

    node[my hexa,fill=RoyalBlue] (Glc1) {GlcN Ac};

    node[right=of Glc1,my hexa,fill=DarkMagenta] (Mur1) {MurN Ac};

    node[right=of Mur1,my hexa,fill=RoyalBlue] (Glc2) {GlcN Ac};

    node[right=of Glc2,my hexa,fill=DarkMagenta] (Mur2) {MurN Ac};

    %

    node[below=of Mur1,my elli,fill=DarkGreen] (L-Ala1) {L-Ala};

    node[below left=8mm and 5mm of L-Ala1,my elli,fill=purple] (D-Glu1)

    {textsc{d}-Glu};

    node[below left=8mm and 5mm of D-Glu1,my elli,fill=DarkRed] (L-Lys1)

    {textsc{l}-Lys};

    node[right=3mm of L-Lys1,my elli,fill=green!80!black] (Gly1) {Gly};

    node[right=3mm of Gly1,my elli,fill=green!80!black] (Gly2) {Gly};

    node[right=3mm of Gly2,my elli,fill=green!80!black] (Gly3) {Gly};

    node[right=3mm of Gly3,my elli,fill=green!80!black] (Gly4) {Gly};

    node[right=3mm of Gly4,my elli,fill=green!80!black] (Gly5) {Gly};

    node[right=3mm of Gly5,my elli,fill=cyan] (D-Ala1) {D-Ala};

    node[below=8mm of L-Lys1,my elli,fill=cyan] (D-Ala2) {D-Ala};

    %

    node[below left=8mm and -5mm of D-Ala1,my elli,fill=DarkRed] (L-Lys2)

    {textsc{l}-Lys};

    node[below left=8mm and -5mm of L-Lys2,my elli,fill=purple] (D-Glu2)

    {textsc{d}-Glu};

    node[below left=8mm and -5mm of D-Glu2,my elli,fill=DarkGreen] (L-Ala2) 

    {L-Ala};

    %

    node[below=of L-Ala2,my hexa,fill=DarkMagenta] (Mur3) {MurN Ac};

    node[left=of Mur3,my hexa,fill=RoyalBlue] (Glc3) {GlcN Ac};

    node[left=of Glc3,my hexa,fill=DarkMagenta] (Mur4) {MurN Ac};

    node[right=of Mur3,my hexa,fill=RoyalBlue] (Glc4) {GlcN Ac};

    %

    draw (Glc1) -- (Mur1) -- (Glc2) -- (Mur2);

    draw (Glc2) -- (L-Ala1) -- (D-Glu1) -- (L-Lys1)

    -- (Gly1) -- (Gly2) -- (Gly3) -- (Gly4) -- (Gly5)

    -- (D-Ala1) -- (L-Lys2) -- (D-Glu2) -- (L-Ala2) -- (Mur3) -- 

    (Glc3) -- (Mur4);

    draw (Mur3) -- (Glc4); 

    draw (L-Lys1) -- (D-Ala2); 

    % 

    node[above=5mm of Gly3,shaded triangle=red] (E4) {E4};

    draw[red,thick,-latex] (E4.south west) -- ($(Gly2)!0.5!(Gly3)$);

    draw[red,thick,-latex] (E4.south east) -- ($(Gly3)!0.5!(Gly4)$);

    path (Gly5) -- (D-Ala1) coordinate[midway](aux);

    node[anchor=south,shaded triangle=red] (E5) at (aux|-E4.south) {E5};

    draw[red,thick,-latex] (E5.south) -- (aux);

    node[right=2mm of D-Glu1] (txt1) {NH$_2$};

    node[left=2mm of D-Glu2] (txt2) {NH$_2$};

    draw (D-Glu1) -- (txt1);

    draw (D-Glu2) -- (txt2);

end{tikzpicture}

end{document}

To make it smaller, you could scale it (e.g. scale=0.8,transform shape) and/or adjust the node distance.

PassOptionsToPackage{svgnames}{xcolor}

documentclass[12pt,a4paper]{scrartcl}

usepackage{tikz, pgf}

usepackage{xltxtra}

renewcommand{familydefault}{sfdefault}

usepackage[T1]{fontenc}

usetikzlibrary{

positioning,

shapes.geometric,

shapes.misc,

shadows.blur,

calc}

newcounter{hexa}

begin{document}

begin{tikzpicture}[node distance=3mm,scale=0.8,transform shape,

every shadow/.style={shadow xshift=-0.5ex,shadow yshift=-0.5ex},

my hexa/.style={blur shadow,chamfered rectangle,chamfered rectangle

xsep=2cm,draw,text=white,path picture={%

draw[white] let p1=($(path picture bounding box.north)-(path picture

bounding box.east)$) in

([xshift=-1pt]path picture bounding box.east)

-- ++(-y1+1pt,y1-1pt) -- ++(2*x1,0);}},

my elli/.style={blur shadow,ellipse,draw,text=white,path picture={%

fill[white] let p1=($(path picture bounding box.north)-(path picture

bounding box.east)$) in ([xshift=-1pt]path picture bounding box.east)

to[out=90,in=0,looseness=0.8] ([yshift=-1pt]path picture bounding box.north)

to[out=0,in=90,looseness=0.7] cycle;

}},

shaded triangle/.style={blur shadow,regular polygon,regular polygon sides=3,shape border rotate=0,

inner sep=1pt,draw,inner color=#1!10,outer color=#1}]

    node[my hexa,fill=RoyalBlue] (Glc1) {GlcN Ac};

    node[right=of Glc1,my hexa,fill=DarkMagenta] (Mur1) {MurN Ac};

    node[right=of Mur1,my hexa,fill=RoyalBlue] (Glc2) {GlcN Ac};

    node[right=of Glc2,my hexa,fill=DarkMagenta] (Mur2) {MurN Ac};

    %

    node[below=of Mur1,my elli,fill=DarkGreen] (L-Ala1) {L-Ala};

    node[below left=8mm and 5mm of L-Ala1,my elli,fill=purple] (D-Glu1)

    {textsc{d}-Glu};

    node[below left=8mm and 5mm of D-Glu1,my elli,fill=DarkRed] (L-Lys1)

    {textsc{l}-Lys};

    node[right=3mm of L-Lys1,my elli,fill=green!80!black] (Gly1) {Gly};

    node[right=3mm of Gly1,my elli,fill=green!80!black] (Gly2) {Gly};

    node[right=3mm of Gly2,my elli,fill=green!80!black] (Gly3) {Gly};

    node[right=3mm of Gly3,my elli,fill=green!80!black] (Gly4) {Gly};

    node[right=3mm of Gly4,my elli,fill=green!80!black] (Gly5) {Gly};

    node[right=3mm of Gly5,my elli,fill=cyan] (D-Ala1) {D-Ala};

    node[below=8mm of L-Lys1,my elli,fill=cyan] (D-Ala2) {D-Ala};

    %

    node[below left=8mm and -2mm of D-Ala1,my elli,fill=DarkRed] (L-Lys2)

    {textsc{l}-Lys};

    node[below left=8mm and -2mm of L-Lys2,my elli,fill=purple] (D-Glu2)

    {textsc{d}-Glu};

    node[below left=8mm and -2mm of D-Glu2,my elli,fill=DarkGreen] (L-Ala2) 

    {L-Ala};

    %

    node[below=of L-Ala2,my hexa,fill=DarkMagenta] (Mur3) {MurN Ac};

    node[left=of Mur3,my hexa,fill=RoyalBlue] (Glc3) {GlcN Ac};

    node[left=of Glc3,my hexa,fill=DarkMagenta] (Mur4) {MurN Ac};

    node[right=of Mur3,my hexa,fill=RoyalBlue] (Glc4) {GlcN Ac};

    %

    draw (Glc1) -- (Mur1) -- (Glc2) -- (Mur2);

    draw (Glc2) -- (L-Ala1) -- (D-Glu1) -- (L-Lys1)

    -- (Gly1) -- (Gly2) -- (Gly3) -- (Gly4) -- (Gly5)

    -- (D-Ala1) -- (L-Lys2) -- (D-Glu2) -- (L-Ala2) -- (Mur3) -- 

    (Glc3) -- (Mur4);

    draw (Mur3) -- (Glc4); 

    draw (L-Lys1) -- (D-Ala2); 

    % 

    node[above=5mm of Gly3,shaded triangle=red] (E4) {E4};

    draw[red,thick,-latex] (E4.south west) -- ($(Gly2)!0.5!(Gly3)$);

    draw[red,thick,-latex] (E4.south east) -- ($(Gly3)!0.5!(Gly4)$);

    path (Gly5) -- (D-Ala1) coordinate[midway](aux);

    node[anchor=south,shaded triangle=red] (E5) at (aux|-E4.south) {E5};

    draw[red,thick,-latex] (E5.south) -- (aux);

    node[right=2mm of D-Glu1] (txt1) {NH$_2$};

    node[left=2mm of D-Glu2] (txt2) {NH$_2$};

    draw (D-Glu1) -- (txt1);

    draw (D-Glu2) -- (txt2);

    draw (Glc1.west) -- ++ (-0.2,0) (Mur2.east) -- ++ (0.2,0) 

    (Glc4.east) -- ++ (0.2,0) (Mur4.west) -- ++ (-0.2,0);

end{tikzpicture}

end{document}

This last version also comes with more realistic shadows, which are opposite to the bright spots.

alternative solution, less fancy (but this can be simple add), with relative positioning of nodes and with some effort to make code short ...

documentclass[12pt,a4paper]{scrartcl}

renewcommand{familydefault}{sfdefault}

usepackage[T1]{fontenc}

usepackage[version=4]{mhchem}



PassOptionsToPackage{svgnames}{xcolor}

usepackage{tikz}

usetikzlibrary{calc, chains,

                positioning,

                shadows,

                shapes.geometric, shapes.symbols

                }

makeatletter

tikzset{suppress join/.code={deftikz@after@path{}}}

makeatother



begin{document}

    begin{tikzpicture}[

    node distance = 8mm and 6mm,

      start chain = going right,

HEX/.style = {signal, signal to=left and right,

              signal pointer angle=120,

              draw=#1, fill=#1!60, text=white,

              minimum height=10mm, inner sep=-3pt,

              drop shadow,

              on chain, join=by -},

ELL/.style = {ellipse, draw=#1, fill=#1!60, text=white,

              minimum height=8mm, drop shadow,

              on chain, join=by -},

CIR/.style = {circle,  draw=olive, ball color=olive!50,

              minimum height=8mm, drop shadow,

              on chain, join=by -},

TRI/.style = {isosceles triangle, draw=red, fill=red!60,

              isosceles triangle apex angle=60,

              shape border rotate=90}

                    ]



    node (h11) [HEX=RoyalBlue]     {GlcNAc};

    node (h12) [HEX=DarkMagenta]   {MurNAc};

    node (h13) [HEX=RoyalBlue]     {GlcNAc};

    node (h14) [HEX=DarkMagenta]   {MurNAc};

        draw (h11.west) -- + (-0.5,0)

              (h14.east) -- + ( 0.5,0);

%

    node (e11) [ELL=teal,suppress join,

                 below=of h12]         {L-Ala};

    node (e12) [ELL=orange,

                 below left=of e11,

                 pin=right:ce{NH2}]  {D-Glu};

    node (e13) [ELL=teal,  below left=of e12]  {L-Lys};

        draw (h12) -- (e11);

    node (c1)  [CIR,suppress join,

                 right=of e13] {Gly};

        draw (e13) -- (c1);

%

    node (c1)  [CIR] {Gly};

    node (c2)  [CIR] {Gly};

    node (c3)  [CIR] {Gly};

    node (c4)  [CIR] {Gly};

    node (e21) [ELL=teal,on chain,join=by -]   {D-Ala};

    node (e22) [ELL=purple,below left=of e21]  {L-Lys};

    node (e23) [ELL=purple!50!black,

                 below left=of e22,

                 pin=left:ce{NH2}]             {D-Glu};

    node (e24) [ELL=teal,below left=of e23]    {L-Ala};

%

    node (h23) [HEX=DarkMagenta,

                 below=of e24]                  {MurNAc};

    node (h22) [HEX=RoyalBlue,left=of h23]     {GlcNAc};

    node (h21) [HEX=DarkMagenta,left=of h22]   {MurNAc};

    node (h24) [HEX=RoyalBlue,suppress join,

                 right=of h23]                  {GlcNAc};

        draw (h21.west) -- + (-0.5,0)

                   (h23) --   (h24)

              (h24.east) -- + ( 0.5,0);

%

    node (A) [CIR,ball color=yellow, suppress join,

               left=of e11] {A};

    node (e25) [ELL=teal,suppress join,

                 below=of e13]    {L-Ala};

        draw (e13) -- (e25);

    node (t1)  [TRI, above=of c3] {E4};

    coordinate (t2) at ($(c4)!0.5!(e21)$);

    node (t3)  [TRI, at=(t2 |- t1)] {E5};

        draw[-latex,red, shorten <=1mm, shorten >=1mm]

            (A)  edge ($(h12)!0.5!(e11)$)

        %

            (t1) edge ($(c2)!0.5!(c3)$)

            (t1) edge ($(c3)!0.5!(c4)$)

            (t3)  to  (t2);

end{tikzpicture}

end{document}