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Arcadia-Science / sourmashconsumr

Working with the outputs of sourmash in R
https://arcadia-science.github.io/sourmashconsumr/
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documenting `plot_taxonomy_annotate_ts_alluvial()` and output #36

Closed taylorreiter closed 2 years ago

taylorreiter commented 2 years ago 
taxonomy_annotate_df <- read_taxonomy_annotate(Sys.glob("~/github/2022-prjna853785-sourmash/outputs/sourmash_taxonomy/SRR*lineages*csv"))

tmp <- readr::read_csv("https://raw.githubusercontent.com/Arcadia-Science/2022-prjna853785-sourmash/main/inputs/metadata.csv") %>%
  select(query_name = run_accession, time = age_months)

plot_taxonomy_annotate_ts_alluvial(taxonomy_annotate_df, time_df = tmp, tax_glom_level = "genus")

image

taylorreiter commented 2 years ago

Change palette:

plot_taxonomy_annotate_ts_alluvial(taxonomy_annotate_df, time_df = tmp, tax_glom_level = "genus") +
  ggthemes::scale_fill_tableau(palette = "Tableau 20")

image

taylorreiter commented 2 years ago

closed by #18