manual colormap plot screws with ticklabels

I haven't found the cause of the label shift yet, I feel like it has something to do with the normalized option though. I'll look into it later.

In the meantime, I wanted to propose a slightly alternative code to yours, which by the way, doesn't have the same problem.

Instead of typing several node commands, you can just do a single addplot ... coordinates so you just need the coordinates themselves and the meta information. I added notes to the additions to explain what they do.

Updates:

• added colormap for text

Output

Code

documentclass{standalone}
usepackage{pgfplots}
definecolor{myyellow}{rgb}{0.96,0.742,0.29}
definecolor{myblue}{rgb}{0.1,0.32,0.738}

pgfplotsset{
    compat=1.17,
    colormap={bluewhiteyellow}{color=(myyellow) color=(white) color=(myblue)},%original
    colormap={mytext}{%
        % black:
        rgb(0000pt)=(0.0,0.0,0.0);
        rgb(1000pt)=(0.0,0.0,0.0);
        % black:
        rgb(1005pt)=(0.0,0.0,0.0);
        rgb(2000pt)=(0.0,0.0,0.0);
        % white
        rgb(2005pt)=(1.0,1.0,1.0);
        rgb(3000pt)=(1.0,1.0,1.0);
        },% a new colormap for the text
}

begin{document}
begin{tikzpicture}
begin{axis}[%
    colormap name={bluewhiteyellow},% for the basic plotting, we use this colormap
    clip=false,
    colorbar,
    x=3em,
    y=3em,
    %xtick=data, % uncommenting these two will remove grid lines for y
    %ytick=data, % also, not needed
    ymin={[normalized]0},
    ymax={[normalized]9},
    xmin={[normalized]0},
    xmax={[normalized]27},
    enlarge x limits={abs=1.5em},
    enlarge y limits={abs=1.5em},
    point meta min=-1,
    point meta max=1,
    grid=both,
    major grid style={draw=none},
    minor tick num=1,
    symbolic x coords={cHq3,cHB,cHW,cHWB,cuBAbs,cuWAbs,cHDD,cHd,cHu,cHq1,cHe,cHl1,cHl3,cll1,cHG,cuGAbs,cG,cqd8,cqq1,cqq11,cqq3,cqq31,cqu1,cqu8,cuH,cud8,cuu,cuu1},
    symbolic y coords={ggHtopev3,ggHtopev2,ggHtopev1,cHl3cll1ev1,cHl1cHeev1,cHucHdcHq1ev1,cHWcHBcHWBcHDDcuWAbscuBAbsev3,cHWcHBcHWBcHDDcuWAbscuBAbsev2,cHWcHBcHWBcHDDcuWAbscuBAbsev1,cHq3},
    %xticklabels={cHq3,cHB,cHW,cHWB,cuBAbs,cuWAbs,cHDD,cHd,cHu,cHq1,cHe,cHl1,cHl3,cll1,cHG,cuGAbs,cG,cqd8,cqq1,cqq11,cqq3,cqq31,cqu1,cqu8,cuH,cud8,cuu,cuu1},
    %yticklabels={ggHtopev3,ggHtopev2,ggHtopev1,cHl3cll1ev1,cHl1cHeev1,cHucHdcHq1ev1,cHWcHBcHWBcHDDcuWAbscuBAbsev3,cHWcHBcHWBcHDDcuWAbscuBAbsev2,cHWcHBcHWBcHDDcuWAbscuBAbsev1,cHq3},
    axis on top,
    x tick label style={scale=1.5,anchor=north east,rotate=45},
    y tick label style={scale=1.5},
    colorbar style={y tick label style={scale=1.5}},
    tick style={draw=none},
    nodes near coords style={% style of the numbers inside marks
        anchor=center,
        font=footnotesize,
        /pgf/number format/fixed,
        /pgf/number format/fixed zerofill,
        /pgf/number format/precision=2,
        color of colormap=pgfplotspointmetatransformed of mytext% we use the new colormap for coloring the text dynamically
    },
    ]
    addplot[
        only marks,
        mark=square*,
        scatter,
        mark size=1.5em,
        scatter src=explicit,% the color for the marks
        nodes near coords*,% the numbers on top
        ] 
        coordinates
        {
            (cHq3,cHq3) [1.00]
            (cHB,cHWcHBcHWBcHDDcuWAbscuBAbsev3) [0.50]
            (cHB,cHWcHBcHWBcHDDcuWAbscuBAbsev2) [0.19]
            (cHB,cHWcHBcHWBcHDDcuWAbscuBAbsev1) [-0.84]
            (cHW,cHWcHBcHWBcHDDcuWAbscuBAbsev3) [-0.08]
            (cHW,cHWcHBcHWBcHDDcuWAbscuBAbsev2) [-0.96]
            (cHW,cHWcHBcHWBcHDDcuWAbscuBAbsev1) [-0.27]
            (cHWB,cHWcHBcHWBcHDDcuWAbscuBAbsev3) [0.86]
            (cHWB,cHWcHBcHWBcHDDcuWAbscuBAbsev2) [-0.20]
            (cHWB,cHWcHBcHWBcHDDcuWAbscuBAbsev1) [0.47]
            (cuBAbs,cHWcHBcHWBcHDDcuWAbscuBAbsev3) [0.06]
            (cuBAbs,cHWcHBcHWBcHDDcuWAbscuBAbsev2) [0.02]
            (cuBAbs,cHWcHBcHWBcHDDcuWAbscuBAbsev1) [-0.05]
            (cuWAbs,cHWcHBcHWBcHDDcuWAbscuBAbsev3) [0.03]
            (cuWAbs,cHWcHBcHWBcHDDcuWAbscuBAbsev1) [-0.02]
            (cHDD,cHWcHBcHWBcHDDcuWAbscuBAbsev3) [0.07]
            (cHd,cHucHdcHq1ev1) [0.26]
            (cHu,cHucHdcHq1ev1) [-0.87]
            (cHq1,cHucHdcHq1ev1) [0.42]
            (cHe,cHl1cHeev1) [-0.62]
            (cHl1,cHl1cHeev1) [0.78]
            (cHl3,cHl3cll1ev1) [0.87]
            (cll1,cHl3cll1ev1) [-0.50]
            (cHG,ggHtopev3) [-0.03]
            (cHG,ggHtopev2) [-0.03]
            (cHG,ggHtopev1) [0.99]
            (cuGAbs,ggHtopev3) [0.67]
            (cuGAbs,ggHtopev2) [0.73]
            (cuGAbs,ggHtopev1) [0.03]
            (cG,ggHtopev3) [0.29]
            (cG,ggHtopev2) [-0.18]
            (cqd8,ggHtopev3) [0.03]
            (cqd8,ggHtopev2) [-0.04]
            (cqq1,ggHtopev3) [0.04]
            (cqq1,ggHtopev2) [-0.03]
            (cqq11,ggHtopev3) [0.25]
            (cqq11,ggHtopev2) [-0.23]
            (cqq3,ggHtopev3) [0.05]
            (cqq3,ggHtopev2) [-0.05]
            (cqq31,ggHtopev3) [0.55]
            (cqq31,ggHtopev2) [-0.54]
            (cqu1,ggHtopev3) [0.01]
            (cqu1,ggHtopev2) [-0.01]
            (cqu8,ggHtopev3) [0.16]
            (cqu8,ggHtopev2) [-0.15]
            (cuH,ggHtopev3) [0.10]
            (cuH,ggHtopev2) [0.06]
            (cud8,ggHtopev3) [0.03]
            (cud8,ggHtopev2) [-0.04]
            (cuu,ggHtopev3) [0.02]
            (cuu,ggHtopev2) [-0.02]
            (cuu1,ggHtopev3) [0.26]
            (cuu1,ggHtopev2) [-0.24]
        };
end{axis}
end{tikzpicture}
end{document}