pRolocVis {pRolocGUI} | R Documentation

## Interactive visualisation of spatial proteomics data

### Description

These functions allow one to explore spatial proteomics data interactively.

### Usage

    pRolocVis(object, app = "pca", fcol, ...)

    pRolocVis_aggregate(object, fcol, groupBy, fig.height = "600px",
      fig.width = "100%", legend.width = "200%", legend.cex = 1,
      nchar = 40, all = TRUE, mirrorX = FALSE, mirrorY = FALSE, ...)

    pRolocVis_classify(object, fcol, scol, mcol = "markers",
      legend.cex = 1, ...)

    pRolocVis_compare(object, fcol1, fcol2, foi, fig.height = "600px",
      fig.width = "100%", legend.width = "200%", legend.cex = 1,
      remap = TRUE, nchar = 40, all = TRUE, mirrorX = FALSE,
      mirrorY = FALSE, ...)

    pRolocVis_pca(object, fcol = "markers", foi, fig.height = "600px",
      fig.width = "100%", legend.width = "200%", legend.cex = 1,
      nchar = 40, all = TRUE, ...)

### Arguments

`object` | An instance of class `MSnSet`, or an `MSnSetList` of length 2 if using `"compare"` application.
`app` | The type of application requested: `"pca"` (default), `"classify"`, `"compare"` or `"aggregate"`. See description below.
`fcol` | The feature meta-data label (`fData` column name) to be used for colouring. Default is `"markers"`. This will correspond to the prediction column if using "classify", or the markers (labelled data) to be plotted otherwise. If set to `NULL`, no annotation is expected.
`...` | Additional parameters passed to `plot2D` for the `"pca"` (such as a different dimensionality reduction technique than PCA, and its arguments), `"classify"`, `"compare"` apps. For the `"aggregate"` app this is for additional parameters to be passed to `combineFeatures`.
`groupBy` | The feature meta-data label (`fData` column name) to be used for summarising the features to be combined.
`fig.height` | Height of the figure. Default is `"600px"`.
`fig.width` | Width of the figure. Default is `"100px"`.
`legend.width` | Width of the legend. Default is `"200%"`.
`legend.cex` | Point character expansion for the the legend. Default is 1.
`nchar` | Maximum number of characters of the markers class names, before their names are truncated. Default is 10.
`all` | If `TRUE` all clusters are displayed on startup, if the total number of clusters is less than including 15. If `FALSE` or otherwise, only the first cluster in the list is displayed.
`mirrorX` | Should the first PC of the second `MSnSet` in `object` be mirrored (default is `FALSE`). Only relevant when `remap` is `FALSE`.
`mirrorY` | Should the second PC of the second `MSnSet` in `object` be mirrored (default is `FALSE`). Only relevant when `remap` is `FALSE`.
`scol` | The feature meta data column containing the classification scores.
`mcol` | The feature meta data column containing the labelled training data, for use with "classify".
`fcol1` | In yhe `compare` app this is the feature meta-data label (fData column name) for the first dataset in the `MSnSetList`. Default is `markers`.
`fcol2` | In the `compare` app this is the feature meta-data label (fData column name) for the second dataset in the `MSnSetList`. Default is `markers`.
`foi` | A `FeaturesOfInterest` or `FoICollection` object.
`remap` | A `logical` indicating whether the second dataset in the `MSnSetList` should be remapped to the first dataset. The default is TRUE.

### Details

The function `pRolocVis` is a wrapper for `pRolocVis_pca`, `pRolocVis_classify`,`pRolocVis_compare`. and `pRolocVis_aggregate`. These Shiny apps allow to explore and analyse interactively spatial proteomics data.

The `pca` Shiny app allows exploration of quantitative data (1) visually through Principle Component Analysis (PCA), (2) protein profiles, and (3) a searchable feature data table, allowing visualisation of particular proteins of interest. (NOTE: This issue on GitHub shows how to use pre-computed coodinates prior to visualisation with the app.)

The `classify` Shiny app is used to visualise classification results and set user-specified thresholds for sub-cellular location predictions.

The `compare` Shiny app is meant for comparing protein localisation between two conditions, or two different experiments, replicates etc. Please note that passing the argument `method` to `...` will not work as it is already specified internally.

The `aggregation` Shiny app displays a scatter plot of the maximum or mean distances within each feature (e.g. protein group) according to its components (e.g. peptides) defined by the `groupBy` argument. A PCA plot of the components is also displayed. It can be used for visualising peptides, PSMs or any other features defined in the feature data of the `MSnSet` and their distributions.

### Value

For the `classify` app a `numeric` vector of thresholds, one per class, to use with `getPredictions`

For the `pca`, `compare` and `aggregate` apps a `character` vector of `featureNames` names of the `object` loaded that have been selected in the app upon application closure.

### Author(s)

Laurent Gatto, Lisa Breckels and Thomas Naake

### See Also

The package vignette: `vignette("pRolocGUI")`.

### Examples

    library("pRoloc")
    library("pRolocdata")
    data(hyperLOPIT2015)
    ## Load the PCA app
    if (interactive()) {
      pRolocVis(hyperLOPIT2015)
    }

    ## Load classification results from hyperLOPIT stored in fData
    if (interactive()) {
      myThreshold <- pRolocVis(hyperLOPIT2015, app = "classify",
                               fcol = "svm.classification",
                               scol = "svm.score")
      newPredictions <- getPredictions(hyperLOPIT2015, fcol = "svm.classification",
                                       scol = "svm.score", t = myThreshold)
    }

    ## Visualise the location and distribution of peptides per protein group
    data("hyperLOPIT2015ms2psm")
    if (interactive()) {
      ## Combine PSM data to peptides
      hl <- combineFeatures(hyperLOPIT2015ms2psm,
                            groupBy = fData(hyperLOPIT2015ms2psm)$Sequence,
                            fun = median)
      ## Visualise peptides according to protein group
      pRolocVis(hl, app = "aggregate", fcol = "markers",
                groupBy = "Protein.Group.Accessions")
    }

[Package pRolocGUI version 1.16.0 Index]