Fix sample.order handling for stacked grouped barplots - order by total stacked height/width

[Copilot]

Fixes a bug in create.barplot() where sample.order = 'increasing'/'decreasing' was incorrectly ordering stacked grouped barplots by the first group's values only, instead of ordering by the total stacked height/width across all groups.

Problem

When creating stacked barplots with groups and using sample.order = 'increasing' or 'decreasing', the bars were ordered based only on the first group's values rather than the sum of all groups for each sample. This resulted in visually incorrect ordering that didn't match user expectations.

For example, with this data:

• Sample A: G1=1, G2=9, G3=0 → total=10 (first value: 1)
• Sample B: G1=5, G2=2, G3=1 → total=8 (first value: 5)
• Sample C: G1=2, G2=1, G3=1 → total=4 (first value: 2)
• Sample D: G1=3, G2=2, G3=1 → total=6 (first value: 3)

The old logic would order by first values: A(1), C(2), D(3), B(5)
The correct logic should order by totals: C(4), D(6), B(8), A(10)

Solution

Modified the sample ordering logic in create.barplot.R to:

1. Detect stacked grouped barplots: Check if stack = TRUE AND groups is not NULL
2. Compute per-sample totals: Sum values across all groups for each sample using na.rm = TRUE
3. Order by totals: Use these computed totals instead of first group values only
4. Preserve existing behavior: Non-stacked plots or plots without groups continue to work as before

The fix handles both vertical orientation (y-values) and horizontal orientation (x-values).

Changes

• R/create.barplot.R: Added conditional logic to compute sample totals for stacked grouped barplots
• tests/testthat/test-stacked-sample-order.R: Added comprehensive tests to verify correct ordering
• NEWS.md: Documented the bug fix

Testing

Added tests that verify:

• sample.order = 'increasing' produces ascending totals left-to-right
• sample.order = 'decreasing' produces descending totals left-to-right
• Both vertical and horizontal orientations work correctly
• Non-stacked and non-grouped plots maintain existing behavior

Fixes #48

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