Add legacy argument compatibility#173
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Summary
Adds a small compatibility layer for legacy argument names that are still used in older examples and issue reports.
getClusters(exp = ...)toobjclusterData(exp = ..., cluster.method = ..., cluster.num = ...)to the current argument namesvisCluster()dotted arguments such asplot.type,markGenes.side,annoTerm.data,line.side,cluster.order,go.col, andadd.barshow_column_names/show_row_namesbefore forwarding arguments toComplexHeatmap::Heatmap()to avoid duplicate-argument errorsThis addresses the legacy-argument failures discussed in issues #160, #167, #168, #169, #170, and #171.
Validation
Rscript -e "setwd('ClusterGVis'); devtools::load_all('.'); testthat::test_dir('tests/testthat')"ggplot2::is.ggplot()andtestthat::expect_is()).R CMD check .\\ClusterGVis --no-manual --no-build-vignetteswas also attempted, but it stops before running code because the current DESCRIPTION is missing generatedAuthor/Maintainerfields from the checker perspective. That metadata issue appears unrelated to this change.