sracipePlotData {sRACIPE} | R Documentation

## Plot sRACIPE data

### Description

Plots heatmap, pca, umap of the data simulated using sRACIPE

### Usage

    sracipePlotData(
      .object,
      plotToFile = FALSE,
      nClusters = 2,
      heatmapPlot = TRUE,
      pcaPlot = TRUE,
      umapPlot = TRUE,
      networkPlot = TRUE,
      clustMethod = "ward.D2",
      col = col,
      distType = "euclidean",
      assignedClusters = NULL,
      corMethod = "spearman",
      ...
    )

    ## S4 method for signature 'RacipeSE'
    sracipePlotData(
      .object,
      plotToFile = TRUE,
      nClusters = 2,
      heatmapPlot = TRUE,
      pcaPlot = TRUE,
      umapPlot = TRUE,
      networkPlot = TRUE,
      clustMethod = "ward.D2",
      col = col,
      distType = "euclidean",
      assignedClusters = NULL,
      corMethod = "spearman",
      ...
    )

### Arguments

`.object` | List A list returned by `sracipeSimulate` function
`plotToFile` | (optional) logical. Default `FALSE`. Whether to save plots to a file.
`nClusters` | (optional) Integer. Default 2. Expected number of clusters in the simulated data. Hierarchical clustering will be used to cluster the data and the the models will be colored in UMAP and PCA plots according to these clustering results. The clusters can be also supplied using `assignedClusters`.
`heatmapPlot` | (optional) logical. Default `TRUE`. Whether to plot hierarchichal clustering.
`pcaPlot` | (optional) logical. Default `TRUE`. Whether to plot PCA embedding.
`umapPlot` | (optional) logical. Default `TRUE`. Whether to plot UMAP embedding
`networkPlot` | (optional) logical. Default `TRUE`. Whether to plot the network.
`clustMethod` | (optional) character. Default `"ward.D2"`. Clustering method for heatmap. See `heatmap.2`
`col` | (optional) Color palette
`distType` | (optional) Distance type. Used only if specified explicitly. Otherwise, 1-cor is used. See `dist`, `hclust`
`assignedClusters` | vector integer or character. Default NULL. Cluster assignment of models.
`corMethod` | (optional) character. Default `"spearman"`. Correlation method for distance function.
`...` | Other arguments

### Value

`RacipeSE` object

### Related Functions

`sracipeSimulate`, `sracipeKnockDown`, `sracipeOverExp`, `sracipePlotData`,

### Examples

    data("demoCircuit")
    ## Not run:
    rSet <- sRACIPE::sracipeSimulate(circuit = demoCircuit, numModels = 20,
    integrateStepSize = 0.1, simulationTime = 30)
    rSet <- sracipePlotData(rSet)

    ## End(Not run)

[Package sRACIPE version 1.3.3 Index]