Arcadia-Science sourmashconsumr issues

Arcadia-Science / sourmashconsumr

Working with the outputs of sourmash in R

https://arcadia-science.github.io/sourmashconsumr/

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issues

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Importing distance.cmp into R

#77 UniAlberta opened 1 month ago
7
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 1 year 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 2 years ago
1
remove themes from ggplots, or at least make sure the same themes are used throughout

#47 taylorreiter closed 2 years 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 2 years ago
1
Add a readme

#44 taylorreiter closed 2 years ago
1
change `plot_taxonomy_annotate_ts_alluvial()` to plot `f_unique_weighted` by default

#43 taylorreiter closed 2 years ago
1
Add example data to package and document the data generation and contents

#42 taylorreiter closed 2 years ago
1
Add to docs that gzip'd sigs can be read in by `read_signature()`

#41 taylorreiter closed 2 years 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 2 years ago
0
refactor `plot_taxonomy_annotate_ts_alluvial()` to allow more flexible column names for `time_df`.

#39 taylorreiter opened 2 years ago
0
refactor `tax_glom_taxonomy_annotate()` to only have piped code block occur once by auto-inheriting `glom_var`

#38 taylorreiter closed 2 years ago
2
Add a function for an alluvial plot when when a time series metagenome was sequenced

#37 taylorreiter closed 2 years ago
1
documenting `plot_taxonomy_annotate_ts_alluvial()` and output

#36 taylorreiter closed 2 years ago
2
Add visualizations for specific use cases like time series or different groups

#35 taylorreiter opened 2 years ago
5
add color to the compare plots

#34 taylorreiter closed 2 years ago
1
code i used to figure out how to the make the sankey plot

#33 taylorreiter closed 2 years ago
0
function to produce a sankey plot from sourmash taxonomy output

#32 taylorreiter closed 2 years 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 2 years ago
0
Plot the outputs of `sourmash gather`

#30 taylorreiter closed 2 years ago
3
Refactor `read_gather` and `read_taxonomy_annotate` to specify col types and test `read_gather`

#29 taylorreiter closed 2 years ago
1
switch `tax_glom*`/agglomeration language to aggregate

#28 taylorreiter opened 2 years ago
0