Refactor summary report generation: improve formatting and update example paths

[AbhirupaGhosh]

No description provided.

[jananiravi]

@AbhirupaGhosh the colors are likely inconsistent. please check!

rest looks good.

[AbhirupaGhosh]

@AbhirupaGhosh the colors are likely inconsistent. please check!

rest looks good.

I changed the color to blue because we had a discussion to change the grey to blue during my poster preparation.

[jananiravi]

@AbhirupaGhosh the colors are likely inconsistent. please check!

rest looks good.

I changed the color to blue because we had a discussion to change the grey to blue during my poster preparation.

I like blue more but tandem changes need to immediately go into amRviz so we don't forget. cc: @eboyer221

[eboyer221]

@AbhirupaGhosh the colors are likely inconsistent. please check!

I like blue more but tandem changes need to immediately go into amRviz so we don't forget. cc: @eboyer221

Confirmed that the color change is already in sync between both amRviz and amRdata. I am pushing a small commit to fix a comment in PHENOTYPE_COLORS that currently reads "Susceptible is intentionally neutral grey" - changing to "muted blue" in the text.

[eboyer221]

I pushed a few commits to help address the comments on this PR for the following issues:

1. @examples erroring in check - I wrapped both generateSummary() and generatePlots() examples in \dontrun{}, since neither data/metadata.parquet nor results/metadata.parquet exist in the package. Verified with tools::Rd2ex() that they now render as ## Not run: and won't execute during R CMD check.
2. cleanMetadata() → cleanMetaData() - the doc reference in generatePlots()'s description didn't match any real function. Corrected it to cleanMetaData(), which is what actually exists in R/data_processing.R and performs the drug_class/drug_abbr join.
3. @return for generateSummary() - now documents that it invisibly returns md_path, matching how generatePlots() documents its return value.

I also reran devtools::document() to sync man/generateSummary.Rd and man/generatePlots.Rd with the updated roxygen comments (NAMESPACE unaffected - no export changes). Manually re-ran both functions end-to-end against data to confirm nothing broke.

[eboyer221]

@jananiravi All three review threads should be resolved now with the fixes I just pushed. Could you take another look when you get a chance to make sure the changes that were requested have now been completed? Thank you.