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Arcadia-Science
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sourmashconsumr
Working with the outputs of sourmash in R
https://arcadia-science.github.io/sourmashconsumr/
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MRG: fix pkgdown install in `devenv.yml`
#76
ctb
closed
1 year ago
2
installation fails on R 4.2.2 on Linux/i386, installed via conda.
#75
ctb
closed
1 year ago
5
MRG: add additional reference for sourmash taxonomic performance
#74
ctb
closed
8 months ago
0
experimental LIN taxonomy integration
#73
bluegenes
opened
1 year ago
0
enable taxonomy plotting with LIN taxonomic framework?
#72
bluegenes
opened
1 year ago
0
`n_unique_kmers` doesn't exist
#71
bluegenes
opened
1 year ago
2
Alpha diversity estimation
#70
gabridinosauro
opened
1 year ago
1
converting tax annotate files to phyloseq object
#69
Htrivett
closed
1 year ago
1
Add more details to the dev docs and update README
#68
taylorreiter
closed
1 year ago
1
Initialize pkgdown and github action to automatically build a documentation site
#67
taylorreiter
closed
1 year ago
2
Update the plot codes and examples so that the plot look can be maniuplated more easily to achieve a specific look
#66
taylorreiter
closed
1 year ago
1
Add developer documentation
#65
taylorreiter
closed
1 year ago
1
small fix for a typo
#64
taylorreiter
closed
1 year ago
0
order sankey plot by most frequently occurring level instead of alphabetical?
#63
taylorreiter
opened
1 year ago
0
add `tidyr::drop_na()` to sankey plot function to avoid errors/warnings and inaccurate plots
#62
taylorreiter
opened
1 year ago
0
add helpful error message for when file path doesnt exist and give hint for sysglob for multiple files
#61
taylorreiter
closed
1 year ago
1
reorder legend of time series alluvial plot so that 'other' always occurs at the last item on the legend
#60
taylorreiter
closed
1 year ago
1
update vignette so it reflects the new palette changing abilities for the taxonomy and gather upset plots
#59
taylorreiter
closed
1 year ago
1
Change the aesthetic of the upset plots to match other plots in the package (`theme_classic()`) and allow palettes to be specified instead of defaulting to Set2
#58
taylorreiter
closed
1 year ago
0
make the default theme for the upper half of all of the upset plots `theme_classic()`
#57
taylorreiter
closed
1 year ago
1
make "other" the last level in ts alluvial plot legend
#56
taylorreiter
closed
1 year ago
1
make the palette for the taxonomy annotate upset plot a user-specifiable parameter
#55
taylorreiter
closed
1 year ago
1
allow users to choose to name from filename or name from query name when plotting things that have multiple samples
#54
taylorreiter
opened
1 year ago
1
add advice to use the `--name` flag in `sketch` to vignette
#53
taylorreiter
closed
1 year ago
1
add a new visualization for sourmash taxonomy annotate that's like the `plot_gather_classified()` plot
#52
taylorreiter
opened
1 year ago
0
Coloring strain plots and why I decided not to implement it for now
#51
taylorreiter
opened
1 year ago
0
Add a function to detect whether multiple strains of the same species are present in a metagenome sample
#50
taylorreiter
closed
1 year ago
0
for `read*()` functions, check if file exists and output and error if it doesn't
#49
taylorreiter
closed
1 year ago
2
Code fixes and new tests for problems I discovered when writing the vignette
#48
taylorreiter
closed
1 year ago
1
remove themes from ggplots, or at least make sure the same themes are used throughout
#47
taylorreiter
closed
1 year ago
2
Create a vignette documenting how to use the sourmashconsumr package
#46
taylorreiter
closed
1 year ago
1
change `read_signature()` to read in from one or many files
#45
taylorreiter
closed
1 year ago
1
Add a readme
#44
taylorreiter
closed
1 year ago
1
change `plot_taxonomy_annotate_ts_alluvial()` to plot `f_unique_weighted` by default
#43
taylorreiter
closed
1 year ago
1
Add example data to package and document the data generation and contents
#42
taylorreiter
closed
1 year ago
1
Add to docs that gzip'd sigs can be read in by `read_signature()`
#41
taylorreiter
closed
1 year ago
1
for `plot_taxonomy_annotate_ts_alluvial()`, add a `show_tax` argument that allows the user to control which taxa are given alluvial ribbons
#40
taylorreiter
opened
1 year ago
0
refactor `plot_taxonomy_annotate_ts_alluvial()` to allow more flexible column names for `time_df`.
#39
taylorreiter
opened
1 year ago
0
refactor `tax_glom_taxonomy_annotate()` to only have piped code block occur once by auto-inheriting `glom_var`
#38
taylorreiter
closed
1 year ago
2
Add a function for an alluvial plot when when a time series metagenome was sequenced
#37
taylorreiter
closed
1 year ago
1
documenting `plot_taxonomy_annotate_ts_alluvial()` and output
#36
taylorreiter
closed
1 year ago
2
Add visualizations for specific use cases like time series or different groups
#35
taylorreiter
opened
1 year ago
5
add color to the compare plots
#34
taylorreiter
closed
1 year ago
1
code i used to figure out how to the make the sankey plot
#33
taylorreiter
closed
1 year ago
0
function to produce a sankey plot from sourmash taxonomy output
#32
taylorreiter
closed
1 year ago
0
for gather upset plot, add another barchart on top that shows the fraction of sample that was taken up by the intersection
#31
taylorreiter
opened
1 year ago
0
Plot the outputs of `sourmash gather`
#30
taylorreiter
closed
1 year ago
3
Refactor `read_gather` and `read_taxonomy_annotate` to specify col types and test `read_gather`
#29
taylorreiter
closed
1 year ago
1
switch `tax_glom*`/agglomeration language to aggregate
#28
taylorreiter
opened
1 year ago
0
Add functions to transform from sourmash taxonomy annotate outputs to phyloseq object
#27
taylorreiter
closed
1 year ago
1
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