library(dplyr)
#> Error in get(paste0(generic, ".", class), envir = get_method_env()) :
#> object 'type_sum.accel' not found
library(ggplot2)
library(qSIP2)
packageVersion("qSIP2")
#> [1] '0.18.4.9000'Background
In qSIP2, you can run the standard EAF workflow with
multiple qsip_data objects at the same time. This vignette
will show you different ways to create and use multiple
qsip_data objects in the same workflow.
Multiple Object Structure
The format for storing multiple qsip_data objects is a
simple named list, where the names are a descriptive but succinct name
for that comparison, and the value is the qsip_data object.
The list can be created in a few different ways, including “by hand”, by
formatting the show_comparison_groups() output, or
providing a dataframe to the dedicated
run_comparison_groups() function. Each of these are
detailed below.
Building the multi qsip_data object “by hand”
In the standard vignette("qSIP_workflow") vignette we
filtered the example object to create “normal” and “drought” objects,
and then proceeded through the workflow with these two objects
independently. However, these two objects can instead be combined using
list() to work with both simultaneously. We can run a
validation function that will return TRUE if the list is
correct.
qsip_normal <- run_feature_filter(example_qsip_object,
unlabeled_source_mat_ids = get_all_by_isotope(example_qsip_object, "12C"),
labeled_source_mat_ids = c("S178", "S179", "S180"),
min_unlabeled_sources = 6, min_labeled_sources = 3,
min_unlabeled_fractions = 5, min_labeled_fractions = 5,
quiet = TRUE
) |>
run_resampling(with_seed = 49, quiet = TRUE, progress = FALSE) |>
run_EAF_calculations()
qsip_drought <- run_feature_filter(example_qsip_object,
unlabeled_source_mat_ids = get_all_by_isotope(example_qsip_object, "12C"),
labeled_source_mat_ids = c("S200", "S201", "S202", "S203"),
min_unlabeled_sources = 6, min_labeled_sources = 3,
min_unlabeled_fractions = 5, min_labeled_fractions = 5,
quiet = TRUE
) |>
run_resampling(with_seed = 50, quiet = TRUE, progress = FALSE) |>
run_EAF_calculations()
qsip_list_1 = list("Normal" = qsip_normal,
"Drought" = qsip_drought)
is_qsip_data_list(qsip_list_1)
#> [1] TRUEThe list objects now holds both qsip_data objects, but
each can be accessed by name (e.g. qsip_list_1$Normal) if
needed. When building by hand, the main benefit of combining multiple
objects together is that you get shared reporting with summary functions
like summarize_EAF_values() and
plot_EAF_values().
summarize_EAF_values(qsip_list_1)#> Confidence level = 0.9| group | feature_id | observed_EAF | mean_resampled_EAF | lower | upper | labeled_resamples | unlabeled_resamples | labeled_sources | unlabeled_sources |
|---|---|---|---|---|---|---|---|---|---|
| Normal | ASV_1 | -0.0153107 | -0.0162090 | -0.0524399 | 0.0239385 | 1000 | 1000 | 3 | 8 |
| Drought | ASV_1 | -0.0333856 | -0.0322146 | -0.0792106 | 0.0219181 | 1000 | 1000 | 4 | 8 |
| Normal | ASV_10 | 0.1126260 | 0.1116218 | 0.0823812 | 0.1405383 | 1000 | 1000 | 3 | 8 |
| Drought | ASV_10 | 0.0543136 | 0.0542462 | 0.0305884 | 0.0788885 | 1000 | 1000 | 4 | 8 |
| Drought | ASV_100 | -0.0892684 | -0.0885048 | -0.1485629 | -0.0283228 | 1000 | 1000 | 3 | 7 |
| Normal | ASV_102 | -0.0080214 | -0.0090271 | -0.0746514 | 0.0546485 | 1000 | 1000 | 3 | 8 |
In the table above, you can see that the feature_id
column is repeated for each group.
plot_EAF_values(qsip_list_1,
top = 50,
error = "ribbon")
#> Confidence level = 0.9
Other helper functions can be used on the list as well.
n_resamples(qsip_list_1)
#> # A tibble: 2 × 2
#> group n_resamples
#> <chr> <dbl>
#> 1 Normal 1000
#> 2 Drought 1000
resample_seed(qsip_list_1)
#> # A tibble: 2 × 2
#> group seed
#> <chr> <dbl>
#> 1 Normal 49
#> 2 Drought 50Dataframe-based multi qsip_data object
Although building the list by hand can be useful in organizing the
output, the functionality of the list structure really shines when you
start with a dataframe of comparisons you want to make. This workflow
will do all of the steps from the initial, unfiltered
qsip_data objects without the need to manually build each
comparison object.
Dataframe Structure
The dataframe has a simple structure, and requires at a minimum three
columns. The group column is the name of the comparison
group, and the unlabeled and labeled columns
are vectors of the source_material_ids to use in the
comparison. Each row of the dataframe will be a separate comparison
group.
Modifying show_comparison_groups() output
Recall that show_comparison_groups() attempts to guess
the relevant comparison groups using the metadata. For the example qsip
object, when grouping by “Moisture” we get
show_comparison_groups(example_qsip_object, group = "Moisture")
#> # A tibble: 2 × 3
#> Moisture `12C` `13C`
#> <chr> <chr> <chr>
#> 1 Normal S149, S150, S151, S152 S178, S179, S180
#> 2 Drought S161, S162, S163, S164 S200, S201, S202, S203The output is already in our desired format, and all that is needed
is some slight tweaking of the column names using
dplyr::select() (or dplyr::rename()).
show_comparison_groups(example_qsip_object, group = "Moisture") |>
dplyr::select("group" = Moisture, "unlabeled" = "12C", "labeled" = "13C")
#> # A tibble: 2 × 3
#> group unlabeled labeled
#> <chr> <chr> <chr>
#> 1 Normal S149, S150, S151, S152 S178, S179, S180
#> 2 Drought S161, S162, S163, S164 S200, S201, S202, S203This dataframe can be passed directly to
run_comparison_groups() to create the multi
qsip_data object. run_comparison_groups()
requires the dataframe and a qsip_data object as the first
two arguments. It has three additional optional arguments that globally
apply to all comparisons: allow_failures
(boolean), seed (integer), and
resamples (integer).
qsip_list_2 = show_comparison_groups(example_qsip_object, group = "Moisture") |>
dplyr::select("group" = Moisture, "unlabeled" = "12C", "labeled" = "13C") |>
run_comparison_groups(example_qsip_object,
seed = 99,
allow_failures = TRUE)
#> Finished groups ■■■■■■■■■■■■■■■■ 50%
#> Finished groups ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 100%
#>
is_qsip_data_list(qsip_list_2)
#> [1] TRUEPlotting the values here should give almost identical results (within
sampling error) to the previous plot, but this time we have enabled the
allow_failures option so we get resampling success as
well.
plot_EAF_values(qsip_list_2,
top = 50,
success_ratio = 0.99,
error = "ribbon")
#> Confidence level = 0.9
Custom dataframe for ultimate control
It is possible to make a dataframe from scratch (e.g. as an excel
spreadsheet) to give even more fine-grain control over each comparison.
Here, rather than setting parameters that will be treated as identical
for all comparisons (like seed = 99 above), here additional
columns can be used to set the values independently per row. An example
dataframe is included in the qSIP2 package called
example_group_dataframe. This dataframe is shown below, but
with some columns temporarily removed for brevity (those columns will be
discussed later).
example_group_dataframe| group | unlabeled | labeled | allow_failures | resamples | seed |
|---|---|---|---|---|---|
| Normal | S149, S150, S151, S152 | S178, S179, S180 | T | 500 | 100 |
| Drought | S161, S162, S163, S164 | S200, S201, S202, S203 | T | 1000 | 101 |
| Drought against all | 12C | S200, S201, S202, S203 | T | 1000 | 102 |
| Normal_S178 | S149, S150, S151, S152 | S178 | T | 1000 | 103 |
| Normal_S179 | S149, S150, S151, S152 | S179 | T | 1000 | 104 |
| Normal_S180 | S149, S150, S151, S152 | S180 | T | 1000 | 105 |
This dataframe shows the customizability of the format, including retaining the ability to use isotope terms like “12C” to grab all source material IDs with that isotope.
qsip_list_3 = example_group_dataframe |>
run_comparison_groups(example_qsip_object)
#> Finished groups ■■■■■■ 17%
#> Finished groups ■■■■■■■■■■■ 33%
#> Finished groups ■■■■■■■■■■■■■■■■ 50%
#> Finished groups ■■■■■■■■■■■■■■■■■■■■■ 67%
#> Finished groups ■■■■■■■■■■■■■■■■■■■■■■■■■■ 83%
#> Finished groups ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 100%
#>
resample_seed(qsip_list_3)
#> # A tibble: 6 × 2
#> group seed
#> <chr> <dbl>
#> 1 Drought 101
#> 2 Drought against all 102
#> 3 Normal 100
#> 4 Normal_S178 103
#> 5 Normal_S179 104
#> 6 Normal_S180 105If you use the additional arguments in
run_comparison_groups() then they will override the values
in the dataframe.
qsip_list_4 = example_group_dataframe |>
run_comparison_groups(example_qsip_object,
seed = 42)
#> Finished groups ■■■■■■ 17%
#> Finished groups ■■■■■■■■■■■ 33%
#> Finished groups ■■■■■■■■■■■■■■■■ 50%
#> Finished groups ■■■■■■■■■■■■■■■■■■■■■ 67%
#> Finished groups ■■■■■■■■■■■■■■■■■■■■■■■■■■ 83%
#> Finished groups ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 100%
#>
resample_seed(qsip_list_4)
#> # A tibble: 6 × 2
#> group seed
#> <chr> <dbl>
#> 1 Drought 42
#> 2 Drought against all 42
#> 3 Normal 42
#> 4 Normal_S178 42
#> 5 Normal_S179 42
#> 6 Normal_S180 42The are 4 additional dataframe columns that
run_comparison_groups() will accept:
min_unlabeled_sources, min_labeled_sources,
min_unlabeled_fractions, and
min_labeled_fractions. These columns are used to set the
minimum number of sources and fractions required for each comparison.
The full example dataframe does additionally contain these columns.
summarize_EAF_values(qsip_list_3) |>
filter(feature_id == "ASV_1")
#> Confidence level = 0.9
#> # A tibble: 6 × 10
#> group feature_id observed_EAF mean_resampled_EAF lower upper
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 Drought ASV_1 -0.0492 -0.0489 -0.108 0.0113
#> 2 Drought against a… ASV_1 -0.0334 -0.0328 -0.0798 0.0195
#> 3 Normal ASV_1 0.000455 0.00138 -0.0326 0.0357
#> 4 Normal_S178 ASV_1 0.0410 0.0421 0.0214 0.0606
#> 5 Normal_S179 ASV_1 -0.0256 -0.0251 -0.0454 -0.00603
#> 6 Normal_S180 ASV_1 -0.0140 -0.0141 -0.0378 0.00564
#> # ℹ 4 more variables: labeled_resamples <int>, unlabeled_resamples <int>,
#> # labeled_sources <int>, unlabeled_sources <int>But, keep in mind that each row of the dataframe will be filtered
differently, and therefore some feature_ids could be
missing from certain comparisons. For example, ASV_311 only appears in
the two “Drought” comparisons.
summarize_EAF_values(qsip_list_3) |>
filter(feature_id == "ASV_311")
#> Confidence level = 0.9
#> # A tibble: 2 × 10
#> group feature_id observed_EAF mean_resampled_EAF lower upper labeled_resamples
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <int>
#> 1 Drou… ASV_311 0.906 0.903 0.650 1.14 1000
#> 2 Drou… ASV_311 0.693 0.693 0.535 0.867 1000
#> # ℹ 3 more variables: unlabeled_resamples <int>, labeled_sources <int>,
#> # unlabeled_sources <int>And although you can plot all together, more than a few objects might
make the plots harder to read. But, because it is a simple list you can
always still access the individual objects if needed using the
$ operator (e.g. qsip_list_3$Drought) or
[] brackets
(e.g. qsip_list_3[c("Drought", "Normal")]).
plot_EAF_values(qsip_list_3[c("Drought", "Normal")],
error = "ribbon",
top = 50)
#> Confidence level = 0.9