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I am trying to render a grid of stones using the code below, however when I remove the stone in m-3-1, the stones above and to the right of it (particularly m-1-5) will be off-center:

documentclass{minimal}

usepackage{tikz}

usetikzlibrary{matrix,shapes.geometric}

newcommandstone[0]{|[circle, shading=ball, ball color=black!80!white, minimum size=.8cm]|} % https://tex.stackexchange.com/a/184068/45824

begin{document}

begin{tikzpicture}

matrix (m) [matrix of nodes,

             anchor=south west,

             column sep={1cm,between origins},

             row sep={1cm,between origins},

             nodes in empty cells,

            ]

{

        &        &        &        & stone \

        &        &        &        &        \

 stone &        &        &        &        \

};

draw[step=1cm,color=gray] (0,0) grid (5,3);

draw[thick,red,->] (m-1-1) -> (m-1-5);

draw[thick,red,->] (m-1-5) -> (m-3-5);

end{tikzpicture}

end{document}

How do I ensure all the stones are aligned correctly?

Cause of issue

First, your "working" code doesn't even output the intended diagram: the circles are not aligned yet

Adding option draw to every nodes in the "not working" code gives us

which can explain the problem: your nodes are aligned correctly, but the matrix itself is not at the right place.

Solution

• Use tikzset
  


• Add option inner sep
  


• Use minimum size option for nodes


• Use anchor center for the arrows (see more below)

documentclass{minimal}

usepackage{tikz}

usetikzlibrary{matrix,shapes.geometric}

tikzset{stone/.style={circle,shading=ball,ball color=black!80!white,minimum size=.8cm}}

newcommandstone{|[stone]|} % https://tex.stackexchange.com/a/184068/45824

begin{document}

begin{tikzpicture}

matrix (m) [matrix of nodes,

             anchor=south west,

             column sep={1cm,between origins},

             row sep={1cm,between origins},

             nodes in empty cells,

             nodes={minimum size=1cm},

             inner sep=0pt

            ]

{

        &        &        &        & stone \

        &        &        &        &        \

        &        &        &        &        \

};

draw[step=1cm,color=gray] (0,0) grid (5,3);

draw[thick,red,->] (m-1-1.center) -> (m-1-5);

draw[thick,red,->] (m-1-5) -> (m-3-5.center);

end{tikzpicture}

end{document}