seqLogo {seqLogo} | R Documentation |
This function takes the 4xW position weight matrix of a DNA sequence motif and plots the corresponding sequence logo.
seqLogo(pwm, ic.scale=TRUE, xaxis=TRUE, yaxis=TRUE, xfontsize=15, yfontsize=15)
pwm |
numeric The 4xW position weight matrix. |
ic.scale |
logical If TRUE, the height of each column is
proportional to its information content. Otherwise, all columns have
the same height. |
xaxis |
logical If TRUE, an X-axis will be plotted. |
yaxis |
logical If TRUE, a Y-axis will be plotted. |
xfontsize |
numeric Font size to be used for the X-axis. |
yfontsize |
numeric Font size to be used for the Y-axis. |
Within each column, the height of a given letter is proportional to its frequency at that position. If ic.scale is TRUE, the height of each column in the plot indicates the information content at that position of the motif. Otherwise, the height of all columns are identical.
None.
Oliver Bembom, bembom@berkeley.edu
mFile <- system.file("Exfiles/pwm1", package="seqLogo") m <- read.table(mFile) pwm <- makePWM(m) seqLogo(pwm)