visualize transcript abundance by group

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Description

visualize transcript abundance by group

Usage

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plotMeans(gene, gown, overall = FALSE, groupvar, groupname = "all",
  meas = c("cov", "FPKM", "rcount", "ucount", "mrcount", "mcov"),
  colorby = c("transcript", "exon"), legend = TRUE,
  labelTranscripts = FALSE)

Arguments

gene

name of gene whose transcripts will be plotted. When using Cufflinks/Tablemaker output, usually of the form "XLOC_######"

gown

ballgown object containing experimental and phenotype data

overall

if TRUE, color features by the overall (experiment-wide) mean rather than a group-specific mean

groupvar

string representing the name of the variable denoting which sample belongs to which group. Can be "none" (if you want the study-wide mean), or must correspond to the name of a column of pData(gown). Usually a categorical variable.

groupname

string representing which group's expression means you want to plot. Can be "none" (if you want the study-wide mean), "all" (if you want a multipanel plot of each group's mean expression), or any of the levels of groupvar.

meas

type of expression measurement to plot. One of "cov", "FPKM", "rcount", "ucount", "mrcount", or "mcov". Not all types are valid for all features. (See description of tablemaker output for more information).

colorby

one of "transcript" or "exon", indicating which feature's abundances should dictate plot coloring.

legend

if TRUE (as it is by default), a color legend is drawn on top of the plot indicating the scale for feature abundances.

labelTranscripts

if TRUE, transcript ids are labeled on the left side of the plot. Default FALSE.

Value

produces a plot of the transcript structure for the specified gene in the current graphics device, colored by study-wide or group-specific mean expression level.

Author(s)

Alyssa Frazee

See Also

plotTranscripts

Examples

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data(bg)
plotMeans('XLOC_000454', bg, groupvar='group', meas='FPKM', 
  colorby='transcript')

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