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precompute vignette
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@Aariq
Aariq committed May 9, 2024
1 parent 3d315fb commit eb1a1dc
Showing 1 changed file with 33 additions and 28 deletions.
61 changes: 33 additions & 28 deletions vignettes/kegg.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,9 @@ library(volcalc)
library(dplyr) #for left_join()
#>
#> Attaching package: 'dplyr'
#> The following object is masked from 'package:ChemmineR':
#>
#> groups
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
Expand Down Expand Up @@ -45,10 +48,10 @@ Let's download .mol files for two compounds, jasmonic acid and methyl jasmonate,
mols <- get_mol_kegg(compound_ids = c("C08491", "C11512"), dir = dl_path)
mols
#> # A tibble: 2 × 2
#> compound_id mol_path
#> <chr> <fs::path>
#> 1 C08491 …6hb9xvfqc5ht80000gp/T/Rtmp4LsL5W/C08491.mol
#> 2 C11512 …6hb9xvfqc5ht80000gp/T/Rtmp4LsL5W/C11512.mol
#> compound_id mol_path
#> <chr> <fs::path>
#> 1 C08491 /var/folders/wr/by_lst2d2fngf67mknmgf4340000gn/T/RtmpKwerlt/C08491.mol
#> 2 C11512 /var/folders/wr/by_lst2d2fngf67mknmgf4340000gn/T/RtmpKwerlt/C11512.mol
```

The data frame returned by `get_mol_kegg()` contains the paths the files were downloaded to in `mol_path`, making for convenient passage on to the `volcalc` function `calc_vol()`.
Expand All @@ -58,10 +61,10 @@ The data frame returned by `get_mol_kegg()` contains the paths the files were do
rvi <- calc_vol(mols$mol_path)
rvi
#> # A tibble: 2 × 5
#> mol_path formula name rvi category
#> <chr> <chr> <chr> <dbl> <fct>
#> 1 /var/folders/pf/rjm3plcx14… C12H18… (-)-… 1.84 moderate
#> 2 /var/folders/pf/rjm3plcx14… C13H20… Meth… 3.81 high
#> mol_path formula name rvi category
#> <chr> <chr> <chr> <dbl> <fct>
#> 1 /var/folders/wr/by_lst2d2fngf67mknmgf4340000gn/T/RtmpKwerlt/C08491.mol C12H18O3 (-)-Jasmonic acid 1.84 moderate
#> 2 /var/folders/wr/by_lst2d2fngf67mknmgf4340000gn/T/RtmpKwerlt/C11512.mol C13H20O3 Methyl jasmonate 3.81 high
```

`calc_vol()` also returns the file paths, so these two data frames can be easily joined.
Expand All @@ -88,14 +91,14 @@ We can download single or multiple compounds with `compound_ids`, but we can als
alam_pathway <- get_mol_kegg(pathway_ids = "map00592", dir = dl_path)
head(alam_pathway)
#> # A tibble: 6 × 3
#> pathway_id compound_id mol_path
#> <chr> <chr> <fs::path>
#> 1 map00592 C00157 …T/Rtmp4LsL5W/map00592/C00157.mol
#> 2 map00592 C01226 …T/Rtmp4LsL5W/map00592/C01226.mol
#> 3 map00592 C04672 …T/Rtmp4LsL5W/map00592/C04672.mol
#> 4 map00592 C04780 …T/Rtmp4LsL5W/map00592/C04780.mol
#> 5 map00592 C04785 …T/Rtmp4LsL5W/map00592/C04785.mol
#> 6 map00592 C06427 …T/Rtmp4LsL5W/map00592/C06427.mol
#> pathway_id compound_id mol_path
#> <chr> <chr> <fs::path>
#> 1 map00592 C00157 /var/folders/wr/by_lst2d2fngf67mknmgf4340000gn/T/RtmpKwerlt/map00592/C00157.mol
#> 2 map00592 C01226 /var/folders/wr/by_lst2d2fngf67mknmgf4340000gn/T/RtmpKwerlt/map00592/C01226.mol
#> 3 map00592 C04672 /var/folders/wr/by_lst2d2fngf67mknmgf4340000gn/T/RtmpKwerlt/map00592/C04672.mol
#> 4 map00592 C04780 /var/folders/wr/by_lst2d2fngf67mknmgf4340000gn/T/RtmpKwerlt/map00592/C04780.mol
#> 5 map00592 C04785 /var/folders/wr/by_lst2d2fngf67mknmgf4340000gn/T/RtmpKwerlt/map00592/C04785.mol
#> 6 map00592 C06427 /var/folders/wr/by_lst2d2fngf67mknmgf4340000gn/T/RtmpKwerlt/map00592/C06427.mol
dim(alam_pathway)
#> [1] 44 3
```
Expand All @@ -105,6 +108,8 @@ Notice that this returns pathway IDs and compound IDs. We can do the same as ab

```r
rvi_path <- calc_vol(alam_pathway$mol_path)
#> Warning in FUN(X[[i]], ...): Possible OpenBabel errors detected and only NAs returned.
#> Run with `validate = FALSE` to ignore this.
```


Expand All @@ -117,17 +122,17 @@ left_join(alam_pathway, rvi_path, by = join_by(mol_path)) %>%
#take just the top 10
slice_head(n = 10)
#> # A tibble: 10 × 6
#> pathway_id compound_id formula name rvi category
#> <chr> <chr> <chr> <chr> <dbl> <fct>
#> 1 map00592 C16310 C6H10O 3-Hex… 7.32 high
#> 2 map00592 C19757 C8H14O2 (3Z)-… 6.75 high
#> 3 map00592 C08492 C6H12O 3-Hex… 6.45 high
#> 4 map00592 C16323 C9H14O 3,6-N… 6.05 high
#> 5 map00592 C11512 C13H20O3 Methy… 3.81 high
#> 6 map00592 C16318 C13H20O3 (+)-7… 3.81 high
#> 7 map00592 C00157 C10H18NO8P Phosp… 2.89 high
#> 8 map00592 C16322 C9H16O3 9-Oxo… 2.77 high
#> 9 map00592 C16343 C17H28O Hepta… 2.69 high
#> 10 map00592 C08491 C12H18O3 (-)-J… 1.84 moderate
#> pathway_id compound_id formula name rvi category
#> <chr> <chr> <chr> <chr> <dbl> <fct>
#> 1 map00592 C16310 C6H10O 3-Hexenal 7.32 high
#> 2 map00592 C19757 C8H14O2 (3Z)-Hex-3-en-1-yl acetate 6.75 high
#> 3 map00592 C08492 C6H12O 3-Hexenol 6.45 high
#> 4 map00592 C16323 C9H14O 3,6-Nonadienal 6.05 high
#> 5 map00592 C11512 C13H20O3 Methyl jasmonate 3.81 high
#> 6 map00592 C16318 C13H20O3 (+)-7-Isomethyljasmonate 3.81 high
#> 7 map00592 C16322 C9H16O3 9-Oxononanoic acid 2.77 high
#> 8 map00592 C16343 C17H28O Heptadecatrienal 2.69 high
#> 9 map00592 C08491 C12H18O3 (-)-Jasmonic acid 1.84 moderate
#> 10 map00592 C16317 C12H18O3 (+)-7-Isojasmonic acid 1.84 moderate
```

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