planning for upgrading in the next 10 days

[huangyh09]

Some draft tasks, please keep adding:

• the selection of l value for the spatial weight matrix (needs to be more automated & more intuitive instructions
• make the z-score method as default (especially for large samples); we may instead mention permutation in the text
• plotting: local ligand/receptor (single color, e.g., white to red)
• trying to replace spatialDE with SparseAEH
• pathway enrichment: make a new function (ideally intro in API): query gene list(s), background gene list, pathway database -> results as data frame (n_pathway - by - columns: total_gene, overlapped_genes, qury_genes, background_mapped_gene, background_upmapped_genes, p-value
• pathway enrichment plotting: results data above -> figure; x-axis: -log10(p), size: overlapped genes
• possibly explore another format of the pl.global_plot(), for example, the p-value is mainly binary for now, not very informative for the significant level
• maybe also consider minimizing the required dependent pkg

[huangyh09]

Any other contributions or contributors are welcome!!