Rnits (version 1.6.2)

plotResults: Plot profiles of top genes/probes

Description

After fit has been applied on Rnits object, plot the profiles of N top ranking genes/probes.

Usage

plotResults(object, id = NULL, fdr = NULL, top = 48, pdf = FALSE, sort.by = "p-value", filename = "TopPlots.pdf", scale_y = NULL)
"plotResults"(object, id = NULL, fdr = NULL, top = 48, pdf = FALSE, sort.by = "p-value", filename = "TopPlots.pdf", scale_y = NULL)

Arguments

object

Rnits object.

id

Names of specific genes or probes to be plotted. Overrides fdr and top argument.

fdr

FDR cut-off plotting top probes or genes. Overrides top argument.

top

Number of top genes or probes whose profile is to be plotted. Default 48.

pdf

Save plot as pdf? Default FALSE.

sort.by

Criteria for sorting top genes or probes. Default 'p-value'.

filename

Name of pdf file. Default topplots.pdf.

scale_y

If 'free', use free scales for plots. Default NULL.

...

Optional arguments to plot

Examples

# load pre-compiled expressionSet object for Ronen and Botstein yeast  chemostat data
data(yeastchemostat)
rnitsobj = build.Rnits(yeastchemostat, logscale = TRUE, normmethod = 'Between')
## Not run: 
# # Fit model using gene-level summarization
# rnitsobj <- fit(rnitsobj, gene.level = TRUE, clusterallsamples = FALSE)
# 
# # Plot top results
# plotResults(rnitsobj, top = 16)
# 
# ## End(Not run)