expressionPlot {cummeRbund} | R Documentation |
A line plot (optionally with confidence intervals) detailing FPKM expression levels across conditions for a given gene(s) or feature(s)
## S4 method for signature 'CuffFeature' expressionPlot(object, logMode=FALSE, pseudocount=1.0, drawSummary=FALSE, sumFun=mean_cl_boot, showErrorbars=TRUE, showStatus=TRUE, replicates=FALSE, facet = TRUE,...)
object |
An object of class ('CuffFeature' or 'CuffGene') |
logMode |
A logical value to draw y-axis (FPKM) on log-10 scale. Default = FALSE. |
pseudocount |
A numeric value added to FPKM to avoid errors on log-10 transformation. |
drawSummary |
A logical valuie. Draws a 'summary' line with mean FPKM values for each condition. |
sumFun |
Function used to determine values for summary line. Default = mean_cl_boot |
showErrorbars |
A logical value whether or not to draw error bars. |
showStatus |
A logical value whether or not to draw visual queues for quantification status of a given gene:condition. Default = TRUE |
replicates |
A logical value whether or not to plot individual replicates or aggregate condition values. |
facet |
A logical value whether or not to facet the plot by feature id (default=TRUE). |
... |
Additional arguments |
None
A ggplot2 plot object
None
Loyal A. Goff
None
data(sampleData) PINK1 # sample CuffFeature object expressionPlot(PINK1) #Line plot of PINK1 FPKM values expressionPlot(PINK1@isoforms) #Line plot of PINK1 FPKM values faceted by isoforms