plot_responses {netresponse} | R Documentation

## plot_responses

### Description

Plot the detected transcriptional responses for a given subnetwork. plot_mode = 'network', xaxis = TRUE, yaxis = TRUE, plot_type = 'twopi', mar = c(5, 4, 4, 2), horiz = TRUE, datamatrix = NULL, scale = FALSE, ...)

### Usage

    plot_responses(
      x,
      subnet.id,
      nc = 3,
      plot_names = TRUE,
      plot_mode = "network",
      xaxis = TRUE,
      yaxis = TRUE,
      plot_type = "twopi",
      mar = c(5, 4, 4, 2),
      horiz = TRUE,
      datamatrix = NULL,
      scale = FALSE,
      ...
    )

### Arguments

`x` | Result from NetResponse (detect.responses function).
`subnet.id` | Subnet id.
`nc` | Number of columns for an array of images.
`plot_names` | Plot node names (TRUE) or indices (FALSE).
`plot_mode` | network: plot responses as a subnetwork graph; matrix, heatmap: plot subnetwork expression matrix. For both, expression of each gene is shown relative to the mean expression level of the gene; boxplot_data: feature-wise boxplots for hard sample-to-response assignments; response.barplot: estimated response centroids as barplot including 95 confidence intervals for the means; pca: PCA projection with estimated centroids and 95 two-dimensional case the original coordinates are used.
`xaxis, yaxis` | Logical. Plot row/column names.
`plot_type` | Network plot mode. For instance, 'neato' or 'twopi'.
`mar` | Figure margins.
`horiz` | Logical. Horizontal barplot_
`datamatrix` | datamatrix
`scale` | scale the phylotypes to unit length (only implemented for plot_mode = 'matrix'
`...` | Further arguments for plot function.

### Value

Used for its side-effects.

### Author(s)

Leo Lahti leo.lahti@iki.fi

### References

See citation('netresponse')

### See Also

`plot_scale`

### Examples

    #
    #res <- detect.responses(D, netw)
    #vis <- plot_responses(res, subnet.id)

[Package netresponse version 1.47.6 Index]