addMapping {OmicNavigator}

Add mapping object

Description

Add mapping object

Usage

addMapping(study, mapping, reset = FALSE)

Arguments

study

An OmicNavigator study created with createStudy

mapping

Feature IDs from models. The input object is a list of named data frames. For each data frame, column names indicate model names while rows indicate featureIDs per model. Features with same index position across columns are treated as mapped across models. For each model, feature IDs must match feature IDs available in the results object of the respective model. 1:N relationships are allowed.

Mapping list elements are required to be named as 'default' or after a model name as provided in addModels(). If a single data frame is provided, this list element is recommended to be named 'default'. For multiple list elements, each with its own data frame, list elements should be named after model name(s) (a single element may still be named 'default'). In that case, when navigating in ON front-end (FE), mapping element related to the selected model in the FE will be used in multimodel plots. If a selected model in FE does not have a corresponding mapping list element, it may still use the mapping list element called 'default' if this is available.

E.g., if in a study there are models "transcriptomics" and "proteomics" and the user wants to create a plot based on data from both, a mapping list should be provided with addMapping(). In this case, the mapping list element may be named 'default'. This should contain a data frame with column names 'transcriptomics' and 'proteomics', where feature IDs that map across models are found in the same row.

reset

Reset the data prior to adding the new data (default: FALSE). The default is to add to or modify any previously added data (if it exists). Setting reset = TRUE enables you to remove existing data you no longer want to include in the study.

Value

Returns the original onStudy object passed to the argument study, but modified to include the newly added data

See Also

getPlottingData, plotStudy