function ax = plotRgaData(tbl, opts)
%PLOTRGADATA Plot RGA partial pressures vs time (companion to plotCryoData).
%
%   ax = plotRgaData(tbl)
%   ax = plotRgaData(tbl, TimeRange=[t1 t2], Masses=["m28" "m18"])
%
%   Plots every channel column of an rgaImportData table against its shared
%   datetime axis. If Masses is given, a second figure shows a stackedplot
%   of those ions over the same time window. Returns a struct with the
%   axes/chart handles.
%
%   Name-value arguments (type "plotRgaData(tbl, " and tab for suggestions):
%     TimeRange  (1x2 datetime) subset window [start end]. Default: full range.
%     Masses     (string) mass labels for the stackedplot, with or without
%                the leading "m": "m28", "28", ["m28" "m18"]. Default: none,
%                i.e. the stackedplot is skipped unless masses are requested.
%
%   By default the y-axis of the first plot is linear (RGA scans contain
%   small near-noise negatives that a log axis cannot show). To switch to
%   the classic semilog view afterwards:
%       set(ax.partial, 'YScale', 'log');
%   (values <= 0 are simply not drawn on a log axis).
%
%   EXAMPLE
%     tbl = rgaImportData('rga1_Jul_01_2026_08-23-06_AM.txt');
%     ax  = plotRgaData(tbl);                             % overlay only
%     ax  = plotRgaData(tbl, TimeRange=[t1 t2]);          % zoom to a window
%     ax  = plotRgaData(tbl, Masses=["m28" "m18" "m44"]); % overlay + ion stack
%
%   See also RGAIMPORTDATA, PLOTCRYODATA, STACKEDPLOT

    arguments
        tbl                       table
        opts.TimeRange (1,2) datetime = [NaT NaT]
        opts.Masses    (1,:) string   = string.empty
    end

    %--- Extract datetime column ---
    dt = tbl.datetime;

    %--- If a real time range was given, subset the table (shared by both plots) ---
    if ~any(isnat(opts.TimeRange))
        mask = dt >= opts.TimeRange(1) & dt <= opts.TimeRange(2);
        tbl  = tbl(mask, :);
        dt   = dt(mask);
    end

    %--- Channel columns = everything except datetime & time_s ---
    chVars = setdiff(tbl.Properties.VariableNames, {'datetime','time_s'}, 'stable');

    units = 'a.u.';
    if isfield(tbl.Properties.UserData, 'units')
        units = tbl.Properties.UserData.units;
    end

    %--- Plot 1: all partial pressures overlaid ---
    figure;
    tl = tiledlayout(1, 1);
    tl.TileSpacing = 'compact';
    tl.Padding     = 'compact';

    ax.partial = nexttile;
    hold on;
    for k = 1:numel(chVars)
        plot(dt, tbl.(chVars{k}), '-', 'LineWidth', 1, ...
            'DisplayName', prettyName(chVars{k}));
    end
    grid on;
    ylabel(sprintf('Partial pressure [%s]', units));
    xlabel('Date & Time');
    title('RGA partial pressures');
    legend('Location', 'best', 'Interpreter', 'none');

    % Match plotCryoData's datetime tick style
    ax.partial.XAxis.TickLabelFormat = 'dd-MMM HH:mm';

    %--- Plot 2: selected ions as a stackedplot (only if masses requested) ---
    ax.stacked = [];
    if ~isempty(opts.Masses)
        sel = selectIons(chVars, opts.Masses);
        if isempty(sel)
            warning('plotRgaData:noIonMatch', ...
                'No channels matched the requested mass label(s): %s', ...
                strjoin(cellstr(opts.Masses), ', '));
        else
            figure;
            ax.stacked = stackedplot(tbl, sel, 'XVariable', 'datetime');
            ax.stacked.Title         = sprintf('Selected ions [%s]', units);
            ax.stacked.XLabel        = 'Date & Time';
            ax.stacked.DisplayLabels = cellfun(@prettyName, sel, 'UniformOutput', false);
            ax.stacked.GridVisible   = 'on';
        end
    end
end

% -------------------------------------------------------------------------
function sel = selectIons(chVars, masses)
% Return the channel names whose mass label matches any entry in masses.
% masses may be given with or without the leading "m" ("m28", "28").
    keep = false(1, numel(chVars));
    for j = 1:numel(masses)
        lbl = masses(j);
        if ~startsWith(lbl, "m")
            lbl = "m" + lbl;
        end
        keep = keep | endsWith(string(chVars), "_" + lbl);
    end
    sel = chVars(keep);
end

% -------------------------------------------------------------------------
function s = prettyName(v)
% "Water_m18" -> "Water (m18)"
    s = regexprep(v, '_m(\d+)$', ' (m$1)');
    s = strrep(s, '_', ' ');
end