Data Structure for {CoreMico}
In order to perform all analyses, data must be in the following structure:
| X | site_1 | site_2 |
|---|---|---|
| OTU_1 | 0 | 20 |
| OTU_2 | 10 | 1 |
| OTU_3 | 20 | 20 |
Where the first row is your taxa names and must be called X and all subsequent rows are numeric containing your taxa counts.
Mean, Variance, Covariance
What is this…
summarise_taxa(arabidopsis)
## # A tibble: 14,890 x 4
## X Mean Variance CV
## <chr> <dbl> <dbl> <dbl>
## 1 OTU_100 0.368 0.707 1.92
## 2 OTU_1000 0.00694 0.00692 0.997
## 3 OTU_10000 0.698 5.85 8.38
## 4 OTU_10002 0.260 0.284 1.09
## 5 OTU_10003 0.00694 0.00692 0.997
## 6 OTU_10006 0.146 0.160 1.10
## 7 OTU_10007 0.00694 0.00692 0.997
## 8 OTU_10008 0.0451 0.0502 1.11
## 9 OTU_1001 0.0694 0.128 1.84
## 10 OTU_10011 0.861 5.30 6.16
## # … with 14,880 more rowsSingle Methods
We can use the built in arabidopsis dataset to look at each of the core methods included in the package thusfar:
Proportion of Sequence Replicates
What this method is, arguments you can change
prop_reps(arabidopsis)
Proportion of Sequence Reads and Replicates
What this method is, arguments you can change
prop_reads_and_reps(arabidopsis)
We encourage collaboration – please submit a PR or issue if you’d like to see more methods included in the package!
All Methods
The main function of the package is combine_methods, a function which prints your taxa table and a logical column for each method if that taxa is included in the column’s method. It also adds the class core_methods to your dataset so it can be used in subsequent plotting:
( combine_arab <- core_methods(arabidopsis) )
## # A tibble: 59,560 x 6
## X Mean Variance CV name value
## <chr> <dbl> <dbl> <dbl> <fct> <dbl>
## 1 OTU_100 0.368 0.707 1.92 Proportion of Sequence Reads 0
## 2 OTU_100 0.368 0.707 1.92 Proportion of Sequence Reads and Repl… 0
## 3 OTU_100 0.368 0.707 1.92 Hard Cut Off 0
## 4 OTU_100 0.368 0.707 1.92 Proportion of Sequence Replicates 0
## 5 OTU_1000 0.00694 0.00692 0.997 Proportion of Sequence Reads 0
## 6 OTU_1000 0.00694 0.00692 0.997 Proportion of Sequence Reads and Repl… 0
## 7 OTU_1000 0.00694 0.00692 0.997 Hard Cut Off 0
## 8 OTU_1000 0.00694 0.00692 0.997 Proportion of Sequence Replicates 0
## 9 OTU_10000 0.698 5.85 8.38 Proportion of Sequence Reads 0
## 10 OTU_10000 0.698 5.85 8.38 Proportion of Sequence Reads and Repl… 0
## # … with 59,550 more rowsPlot
This function takes on the output of core_methods. This plot…….. The function has one neccessary argument, combined_otu_data, but you can include the low and high colors for hex fills as well as a more informative legend title:
core_plots(combine_arab, high= "#1B301E", low = "#E1E4E1", legend_title = "Arabidopsis Taxa Count")
