Plot sRACIPE data — sracipePlotData • sRACIPE
Description: Plots heatmap, pca, umap of the data simulated using sRACIPE

# Plot sRACIPE data

Source: `R/AllGenerics.R`, `R/methods.R`
`sracipePlotData.Rd`

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

    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 RacipeSE
    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",
      ...
    )

## 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")
    if (FALSE) {
    rSet <- sRACIPE::sracipeSimulate(circuit = demoCircuit, numModels = 20,
    integrateStepSize = 0.1, simulationTime = 30)
    rSet <- sracipePlotData(rSet)
    }