Skip to content

Commit

Permalink
v0.0.1
Browse files Browse the repository at this point in the history
  • Loading branch information
@abichat
abichat committed Mar 7, 2024
1 parent 3b1694e commit c88f6c6
Show file tree
Hide file tree
Showing 3 changed files with 50 additions and 50 deletions.
2 changes: 1 addition & 1 deletion DESCRIPTION
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: scimo
Title: Extra Recipes Steps For Dealing With Omics Data
Version: 0.0.0.9000
Version: 0.0.1
Authors@R: c(
person("Antoine", "BICHAT", , "[email protected]", role = c("aut", "cre"),
comment = c(ORCID = "0000-0001-6599-7081")),
Expand Down
4 changes: 3 additions & 1 deletion NEWS.md
View file
Original file line number Diff line number Diff line change
@@ -1 +1,3 @@
# scimo 0.0.0.9000
# scimo 0.0.1

* First release of **scimo**.
94 changes: 46 additions & 48 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
<!-- badges: start -->

[![experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![packageversion](https://img.shields.io/badge/version-0.0.0.9000-orange.svg)](commits/master)
[![packageversion](https://img.shields.io/badge/version-0.0.1-orange.svg)](commits/master)
[![R-CMD-check](https://github.com/abichat/scimo/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/abichat/scimo/actions/workflows/R-CMD-check.yaml)
<!-- badges: end -->

Expand Down Expand Up @@ -34,37 +34,37 @@ data("cheese_abundance", "cheese_taxonomy")

cheese_abundance
#> # A tibble: 9 × 77
#> sample cheese rind_type asv_01 asv_02 asv_03 asv_04 asv_05 asv_06 asv_07
#> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 sample1-1 Saint-Ne… Natural 1 0 38 40 1 2 31
#> 2 sample1-2 Saint-Ne… Natural 3 4 38 61 4 4 48
#> 3 sample1-3 Saint-Ne… Natural 28 16 33 23 31 29 21
#> 4 sample2-1 Livarot Washed 0 2 1 0 5 1 0
#> 5 sample2-2 Livarot Washed 0 0 4 0 1 1 2
#> 6 sample2-3 Livarot Washed 0 1 2 0 2 1 0
#> 7 sample3-1 Epoisses Washed 4 2 3 0 2 5 0
#> 8 sample3-2 Epoisses Washed 0 0 0 0 0 0 0
#> 9 sample3-3 Epoisses Washed 0 0 1 0 0 0 2
#> # ℹ 67 more variables: asv_08 <dbl>, asv_09 <dbl>, asv_10 <dbl>, asv_11 <dbl>,
#> # asv_12 <dbl>, asv_13 <dbl>, asv_14 <dbl>, asv_15 <dbl>, asv_16 <dbl>,
#> # asv_17 <dbl>, asv_18 <dbl>, asv_19 <dbl>, asv_20 <dbl>, asv_21 <dbl>,
#> # asv_22 <dbl>, asv_23 <dbl>, asv_24 <dbl>, asv_25 <dbl>, asv_26 <dbl>,
#> # asv_27 <dbl>, asv_28 <dbl>, asv_29 <dbl>, asv_30 <dbl>, asv_31 <dbl>,
#> # asv_32 <dbl>, asv_33 <dbl>, asv_34 <dbl>, asv_35 <dbl>, asv_36 <dbl>,
#> # asv_37 <dbl>, asv_38 <dbl>, asv_39 <dbl>, asv_40 <dbl>, asv_41 <dbl>, …
#> sample cheese rind_type asv_01 asv_02 asv_03 asv_04 asv_05 asv_06 asv_07 asv_08 asv_09 asv_10 asv_11 asv_12 asv_13 asv_14 asv_15 asv_16
#> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 sample1-1 Saint-Ne… Natural 1 0 38 40 1 2 31 8 15 20076 160 92 64 24 51 0
#> 2 sample1-2 Saint-Ne… Natural 3 4 38 61 4 4 48 14 20 32101 403 143 165 39 104 1
#> 3 sample1-3 Saint-Ne… Natural 28 16 33 23 31 29 21 1 7 12921 134 53 55 16 45 2
#> 4 sample2-1 Livarot Washed 0 2 1 0 5 1 0 0 0 7823 2 0 0 42 0 2
#> 5 sample2-2 Livarot Washed 0 0 4 0 1 1 2 0 0 6740 4 1 0 45 0 1
#> 6 sample2-3 Livarot Washed 0 1 2 0 2 1 0 0 0 7484 6 1 0 43 0 7
#> 7 sample3-1 Epoisses Washed 4 2 3 0 2 5 0 0 0 2486 1 1 1 23 0 24
#> 8 sample3-2 Epoisses Washed 0 0 0 0 0 0 0 0 0 3686 2 0 0 28 0 54
#> 9 sample3-3 Epoisses Washed 0 0 1 0 0 0 2 0 0 2988 2 1 0 22 0 36
#> # ℹ 58 more variables: asv_17 <dbl>, asv_18 <dbl>, asv_19 <dbl>, asv_20 <dbl>, asv_21 <dbl>, asv_22 <dbl>, asv_23 <dbl>, asv_24 <dbl>,
#> # asv_25 <dbl>, asv_26 <dbl>, asv_27 <dbl>, asv_28 <dbl>, asv_29 <dbl>, asv_30 <dbl>, asv_31 <dbl>, asv_32 <dbl>, asv_33 <dbl>,
#> # asv_34 <dbl>, asv_35 <dbl>, asv_36 <dbl>, asv_37 <dbl>, asv_38 <dbl>, asv_39 <dbl>, asv_40 <dbl>, asv_41 <dbl>, asv_42 <dbl>,
#> # asv_43 <dbl>, asv_44 <dbl>, asv_45 <dbl>, asv_46 <dbl>, asv_47 <dbl>, asv_48 <dbl>, asv_49 <dbl>, asv_50 <dbl>, asv_51 <dbl>,
#> # asv_52 <dbl>, asv_53 <dbl>, asv_54 <dbl>, asv_55 <dbl>, asv_56 <dbl>, asv_57 <dbl>, asv_58 <dbl>, asv_59 <dbl>, asv_60 <dbl>,
#> # asv_61 <dbl>, asv_62 <dbl>, asv_63 <dbl>, asv_64 <dbl>, asv_65 <dbl>, asv_66 <dbl>, asv_67 <dbl>, asv_68 <dbl>, asv_69 <dbl>,
#> # asv_70 <dbl>, asv_71 <dbl>, asv_72 <dbl>, asv_73 <dbl>, asv_74 <dbl>

glimpse(cheese_taxonomy)
#> Rows: 74
#> Columns: 9
#> $ asv <chr> "asv_01", "asv_02", "asv_03", "asv_04", "asv_05", "asv_06", "a…
#> $ lineage <chr> "k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Dothideales|f__D…
#> $ kingdom <chr> "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi",…
#> $ phylum <chr> "Ascomycota", "Ascomycota", "Ascomycota", "Ascomycota", "Ascom…
#> $ class <chr> "Dothideomycetes", "Eurotiomycetes", "Eurotiomycetes", "Euroti…
#> $ order <chr> "Dothideales", "Eurotiales", "Eurotiales", "Eurotiales", "Euro…
#> $ family <chr> "Dothioraceae", "Aspergillaceae", "Aspergillaceae", "Aspergill…
#> $ genus <chr> "Aureobasidium", "Aspergillus", "Penicillium", "Penicillium", …
#> $ species <chr> "Aureobasidium Group pullulans", "Aspergillus fumigatus", "Pen…
#> $ asv <chr> "asv_01", "asv_02", "asv_03", "asv_04", "asv_05", "asv_06", "asv_07", "asv_08", "asv_09", "asv_10", "asv_11", "asv_12", "asv_…
#> $ lineage <chr> "k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Dothideales|f__Dothioraceae|g__Aureobasidium|s__Aureobasidium_Group_pullulans",…
#> $ kingdom <chr> "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi",…
#> $ phylum <chr> "Ascomycota", "Ascomycota", "Ascomycota", "Ascomycota", "Ascomycota", "Ascomycota", "Ascomycota", "Ascomycota", "Ascomycota",…
#> $ class <chr> "Dothideomycetes", "Eurotiomycetes", "Eurotiomycetes", "Eurotiomycetes", "Eurotiomycetes", "Eurotiomycetes", "Eurotiomycetes"…
#> $ order <chr> "Dothideales", "Eurotiales", "Eurotiales", "Eurotiales", "Eurotiales", "Eurotiales", "Eurotiales", "Eurotiales", "Eurotiales"…
#> $ family <chr> "Dothioraceae", "Aspergillaceae", "Aspergillaceae", "Aspergillaceae", "Aspergillaceae", "Aspergillaceae", "Aspergillaceae", "…
#> $ genus <chr> "Aureobasidium", "Aspergillus", "Penicillium", "Penicillium", "Penicillium", "Penicillium", "Penicillium", "Penicillium", "Pe…
#> $ species <chr> "Aureobasidium Group pullulans", "Aspergillus fumigatus", "Penicillium Group camemberti caseifulvum fuscoglaucum commune", "P…
```

``` r
Expand All @@ -74,8 +74,7 @@ head(list_family, 2)
#> [1] "asv_02" "asv_03" "asv_04" "asv_05" "asv_06" "asv_07" "asv_08" "asv_09"
#>
#> $Debaryomycetaceae
#> [1] "asv_10" "asv_11" "asv_12" "asv_13" "asv_14" "asv_15" "asv_16" "asv_17"
#> [9] "asv_18" "asv_19" "asv_20" "asv_21" "asv_22"
#> [1] "asv_10" "asv_11" "asv_12" "asv_13" "asv_14" "asv_15" "asv_16" "asv_17" "asv_18" "asv_19" "asv_20" "asv_21" "asv_22"
```

The following recipe will
Expand All @@ -98,7 +97,7 @@ rec <-

rec
#>
#> ── Recipe ──────────────────────────────────────────────────────────────────────
#> ── Recipe ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#>
#> ── Inputs
#> Number of variables by role
Expand All @@ -109,25 +108,24 @@ rec
#> Training data contained 9 data points and no incomplete rows.
#>
#> ── Operations
#> • Aggregation of: asv_01, asv_02, asv_03, asv_04, asv_05, ... | Trained
#> • TSS normalization on: Aspergillaceae and Debaryomycetaceae, ... | Trained
#> • Kruskal filtering against cheese on: Aspergillaceae, ... | Trained
#> • Aggregation of: asv_01, asv_02, asv_03, asv_04, asv_05, asv_06, asv_07, asv_08, asv_09, asv_10, asv_11, asv_12, asv_13, ... | Trained
#> • TSS normalization on: Aspergillaceae, Debaryomycetaceae, Dipodascaceae, Dothioraceae, Lichtheimiaceae, Metschnikowiaceae, ... | Trained
#> • Kruskal filtering against cheese on: Aspergillaceae, Debaryomycetaceae, Dipodascaceae, Dothioraceae, Lichtheimiaceae, ... | Trained

juice(rec)
#> # A tibble: 9 × 8
#> sample rind_type cheese Debaryomycetaceae Dipodascaceae Saccharomycetaceae
#> <fct> <fct> <fct> <dbl> <dbl> <dbl>
#> 1 sample1-1 Natural Saint-… 0.719 0.0684 0.113
#> 2 sample1-2 Natural Saint-… 0.715 0.0725 0.119
#> 3 sample1-3 Natural Saint-… 0.547 0.277 0.0938
#> 4 sample2-1 Washed Livarot 0.153 0.845 0.000854
#> 5 sample2-2 Washed Livarot 0.150 0.848 0.00106
#> 6 sample2-3 Washed Livarot 0.160 0.837 0.00108
#> 7 sample3-1 Washed Epoiss… 0.0513 0.944 0.00327
#> 8 sample3-2 Washed Epoiss… 0.0558 0.941 0.00321
#> 9 sample3-3 Washed Epoiss… 0.0547 0.942 0.00329
#> # ℹ 2 more variables: `Saccharomycetales fam Incertae sedis` <dbl>,
#> # Trichosporonaceae <dbl>
#> sample rind_type cheese Debaryomycetaceae Dipodascaceae Saccharomycetaceae Saccharomycetales fam Incertae sedi…¹ Trichosporonaceae
#> <fct> <fct> <fct> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 sample1-1 Natural Saint-Nectaire 0.719 0.0684 0.113 0.00130 0.000702
#> 2 sample1-2 Natural Saint-Nectaire 0.715 0.0725 0.119 0.000801 0.000628
#> 3 sample1-3 Natural Saint-Nectaire 0.547 0.277 0.0938 0.000289 0.00239
#> 4 sample2-1 Washed Livarot 0.153 0.845 0.000854 0 0.000349
#> 5 sample2-2 Washed Livarot 0.150 0.848 0.00106 0 0.000176
#> 6 sample2-3 Washed Livarot 0.160 0.837 0.00108 0 0.000212
#> 7 sample3-1 Washed Epoisses 0.0513 0.944 0.00327 0 0.000140
#> 8 sample3-2 Washed Epoisses 0.0558 0.941 0.00321 0 0.000176
#> 9 sample3-3 Washed Epoisses 0.0547 0.942 0.00329 0 0.000125
#> # ℹ abbreviated name: ¹​`Saccharomycetales fam Incertae sedis`
```

To see which variables are kept and the associated p-values, you can use
Expand Down Expand Up @@ -177,7 +175,7 @@ recipe(pedcan_expression) %>%
update_role(-disease, new_role = "predictor") %>%
step_select_cv(all_numeric_predictors(), prop_kept = 0.1)
#>
#> ── Recipe ──────────────────────────────────────────────────────────────────────
#> ── Recipe ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#>
#> ── Inputs
#> Number of variables by role
Expand Down

0 comments on commit c88f6c6

Please sign in to comment.