Package index • qSIP2

qSIP Data Objects

qsip_data(): qSIP master data class

qsip_source_data(): qSIP source data class

qsip_sample_data(): qSIP sample data class

qsip_feature_data(): qSIP feature table class

qSIP2 EAF Workflow

show_comparison_groups(): Show comparison groups

run_feature_filter(): Filter features in a qSIP data object

run_resampling(): Resample WAD values

run_EAF_calculations(): Calculate EAF values

summarize_EAF_values(): Summarize the observed and resampled EAF values

run_comparison_groups(): Run comparison groups

qSIP2 Growth Workflow

get_N_total_it(): Calculate total abundances at timepoint t

run_growth_calculations(): Run growth calculations

summarize_growth_values(): Summarize growth values

Helper Functions

infer_source_data(): Generate a source data frame from a sample data frame

add_isotopolog_label(): Add isotopolog_label to source data

remove_isotopolog_label(): Remove isotopolog_label from "MISIPified" data

get_all_by_isotope(): Get source_mat_ids meeting certain isotope conditions

get_dataframe: Return the original dataframe from a qsip_feature_data object

get_resample_counts(): Get counts of successful resampling

get_resample_data(): Get dataframe of resampled data

get_feature_ids(): Return the feature_ids in a qsip object

get_filtered_feature_summary(): Return filtering info for a specific feature ID

get_source_mat_ids(): Return the source_mat_ids in a qsip object

get_growth_data(): Get dataframe of resampled growth data

resample_seed(): Seed used in resampling

n_resamples(): Number of resamples

add_gradient_pos_rel_amt(): Add gradient_pos_rel_amt to data

add_taxonomy(): Add a taxonomy table to qSIP abundance data

correct_gradient_pos_density(): Correct sample density values using gradient position information

show_unshared_ids(): Show missing source_mat_ids and sample_ids

is_qsip_data(): Check object is qsip_data type

is_qsip_data_list(): Validate a multi-qsip list object

is_qsip_filtered(): Validate a qsip object has been filtered

is_qsip_resampled(): Validate a qsip object has been resampled

is_qsip_EAF(): Validate a qsip object has EAF values

is_qsip_growth(): Validate a qsip object has been run through growth workflow

Plots and Visualizations

plot_sample_curves(): Plot qSIP sample data density curves

plot_source_wads(): Plot the source WADs by isotope

plot_density_outliers(): Cook's outlier detection on gradient positions vs densities

plot_feature_curves(): Plot qSIP feature data density curves

plot_filter_results(): Plot the results of filtering features

plot_feature_occurrence(): Plot occurrence of features in samples

plot_successful_resamples(): Plot the number of successful resamples for each feature_id

plot_feature_resamplings(): Plot the resampled EAFs for each feature

plot_EAF_values(): Plot EAF and confidence intervals

plot_growth_values(): Plot growth values

Spike-In Controls

jgi_source_df(): Make a source dataframe from JGI proposal file

jgi_sample_df(): Make a sample dataframe from JGI proposal file

jgi_feature_df(): Make a feature dataframe from a JGI coverage file

fit_regression_model(): Fit regression model to spike-in control data

jgi_normalize_features(): asdf

get_normalized_features(): Get normalized features from jgi_normalize_features

Datasets

example_source_df: Example Source Dataframe

example_sample_df: Example Sample Dataframe

example_feature_df: Example Feature Abundance Dataframe

example_source_object: Example qSIP Source Object

example_sample_object: Example qSIP Sample Object

example_feature_object: Example qSIP Feature Object

example_qsip_object: Example qSIP Object

example_group_dataframe: Example data frame for run_comparison_groups()

example_qsip_growth_object: Example qSIP Growth Object

example_qsip_growth_t0: Example qSIP Time Zero Growth Dataframe