## S3 method for class 'CCProfile,missing':
plot(x, col=c("red", "blue"),
standardize=TRUE, shades=NULL, legend="default",
legendPos="topright", xlab="", ylab="weight",
lwd.profile=1, lwd.axis=1, las=1,
heptads=TRUE, annotate=TRUE, ...)CCProfile plotFALSE, the profile
values $s_i$ are displayed as they are with the value
$y=-b/L$ superimposed as a light gray line. If TRUE
(default), the profile(s) is/are shifted by the baseline values
$-b/L$ and the light
gray line is displayed at $y=0$.shades[1] and
shades[2], respectively."default", the names of the
sequences/profiles are used. If no names are available, the profiles
are simply enumerated (as long as two profiles should be plot
together; if only a single unnamed profile is to be plotted, no
legend is shown). If legend is an empty string, no legend
is displayed at all.legend
is specified). Can either be a vector with
coordinates or a single keyword like
legend).lwd in parlwd in parparTRUE (default), the heptad structure
is indicated by vertical light gray lines separating the different
heptads. Heptad irregularities are indicated with red lines.TRUE (default), the heptad annotation
information is shown in the center of the plot.plot method from the
plot function displays a prediction profile as a step
function over the sequence with the steps connected by vertical lines.
The sequence and the heptad register are visualized below and above
the profile, respectively. The baseline value $-b/L$ and the light
gray line has the following meaning: It is obvious that we can rewrite$$f(x)=b+\sum\limits_{i=1}^{L} s_i(x)$$
as
$$f(x)=\sum\limits_{i=1}^{L} (s_i(x) - (-\frac{b}{L}))$$
so the discriminant function value $f(x)$ can be understood as the sum of values $s_i(x) - (-\frac{b}{L})$, i.e. the area between the constant value $-b/L$ and the prediction profile. If the area above the light gray line is greater than the area below the light gray line, the sequence is predicted as trimer, otherwise as dimer.
If plot is called for a plot function tolerates
profiles/sequences with different lengths and/or unaligned heptad
registers, it is obvious that the superimposition of profiles of
two unaligned, unrelated sequences makes little sense.
The plot functions gives an error if is called for a
The given function is only a wrapper around the
plot function provided
by the heptads) and the heptad annotation
(argument annotate) are displayed by default.
Moreover, presently, no legend is displayed by default if a
single profile is plotted for an unnamed sequence.
Mahrenholz, C.C., Abfalter, I.G., Bodenhofer, U., Volkmer, R., and Hochreiter, S. (2011) Complex networks govern coiled coil oligomerization - predicting and profiling by means of a machine learning approach. Mol. Cell. Proteomics 10(5):M110.004994. DOI: 10.1074/mcp.M110.004994
Palme, J., Hochreiter, S., and Bodenhofer, U. (2015) KeBABS: an R package for kernel-based analysis of biological sequences. Bioinformatics 31(15):2574-2576. DOI: 10.1093/bioinformatics/btv176
procoil, CCModel CCProfile ## predict oligomerization of GCN4 wildtype
GCN4wt <- predict(PrOCoilModel,
"MKQLEDKVEELLSKNYHLENEVARLKKLV",
"abcdefgabcdefgabcdefgabcdefga")
## plot profile
plot(GCN4wt)
## define two GCN4 mutations
GCN4mSeq <- c("GCN4wt" ="MKQLEDKVEELLSKNYHLENEVARLKKLV",
"GCN4_N16I_L19N"="MKQLEDKVEELLSKIYHNENEVARLKKLV")
GCN4mReg <- rep("abcdefgabcdefgabcdefgabcdefga", 2)
## predict oligomerization
GCN4mut <- predict(PrOCoilModel, GCN4mSeq, GCN4mReg)
## overlay plot of the two profiles
plot(GCN4mut)Run the code above in your browser using DataLab