plot_responses: plot_responses

In antagomir/netresponse: Functional Network Analysis

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 [e-mail]

References

See citation('netresponse')

See Also

plot_scale

Examples

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

antagomir/netresponse documentation built on March 30, 2023, 7:24 a.m.