plot_responses: 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

Result from NetResponse (detect.responses function).

subnet.id

Subnet id.

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 95confidence intervals for the means; pca: PCA projection with estimated centroids and 95two-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

scale

scale the phylotypes to unit length (only implemented for plot_mode = "matrix"

...

Further arguments for plot function.

Value

Used for its side-effects.

References

See citation("netresponse")

Examples

Run this code

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