TODO_shiny_opt.md

In jmw86069/splicejam: Analysis and Visualization of Gene Splice Variants and Transcriptome Data

shiny todo optimization/performance tuning ideas:

• UNNECESSARY: consider how to keep sashimi plot updates to one pass, preventing sample_id and gene changes from being out of sync, and triggering a partial update to the plot before both are ready.

• get_sashimi_data() might be that step

• UNNECESSARY: move memoise function definitions outside the reactive({}) blocks

• e.g. prepareSashimi_m

• also check use_memoise and create non-memoise version

• UNNECESSARY: move gene_exon_structure gene2gg() into separate reactive function that depends upon:

show_gene_model_d() # if FALSE then return NULL
flatExonsByGene1 <- get_flat_gene_exons_plot();
gene <- get_active_gene();
get_gene_coords()
exonLabelSize=14 + exon_label_size_d() + font_sizing_d()

• consider moving plotly sashimi creation into separate function

gg_ly <- get_plotly_sashimi() # reactive

• consider moving ggplot2 sashimi creation into separate function

gg_ly <- getgg_plot2_sashimi() # reactive

• COMPLETE: allow gene/transcript/exon model panel height to be adjusted

• TODO: when there are 2+ panel columns, display gene model below each column

• TODO: when "show detected transcripts" is not checked, re-calculate flat exons for that gene

• organize dependency tree and see if there are shortcuts in the process

• File issue with ggrepel, ask if labels outside plot range can be hidden, for example when using coord_cartesian() to limit visual range.

jmw86069/splicejam documentation built on Nov. 4, 2024, 10:53 a.m.