bio3d (version 2.2-4)

plot.enma: Plot eNMA Results

Description

Produces a plot of atomic fluctuations of aligned normal modes.

Usage

"plot"(x,  pdbs = NULL, conservation = NULL, variance = FALSE,  spread = FALSE, offset = 1, col = NULL, signif = FALSE, pcut = 0.005, qcut = 0.04, xlab = "Alignment Position", ylab=c("Fluctuations", "Fluct.variance", "Seq.conservation"), xlim = NULL, ylim = NULL, mar = c(4, 5, 2, 2), ...)

Arguments

x

the results of ensemble NMA obtained with nma.pdbs. Alternatively, a matrix in the similar format as enma$fluctuations can be provided.

pdbs

an object of class ‘pdbs’ in which the ‘enma’ object x was obtained from. If provided SSE data of the first structure of pdbs will drawn.

conservation

logical, if TRUE sequence conservation is plotted. Alternatively, provide the conservation assement method (‘similarity’, ‘identity’, ‘entropy22’, or ‘entropy10’). A numeric vector of residue conservation values are also allowed.

variance

logical, if TRUE fluctuation variance is plotted.

spread

logical, if TRUE the fluctuation profiles are spread - i.e. not on top of each other.

offset

numerical offset value in use when ‘spread=TRUE’.

col

a character vector of plotting colors. Used also to group fluctuation profiles when ‘spread=TRUE’. NA values in col will omit the corresponding fluctuation profile in the plot.

signif

logical, if TRUE significance of difference is plotted.

pcut

P-value cutoff for the significance.

qcut

Cutoff for the minimal difference of mean fluctuation to plot the significance.

xlab

a label for the x axis.

ylab

labels for the y axes.

mar

a numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot.

xlim

the x limits of the plot.

ylim

the y limits of the plot.

...

extra plotting arguments passed to plot.bio3d that effect the atomic fluctuations plot only.

Value

Called for its effect.

Details

plot.enma produces a fluctuation plot of aligned nma objects.

References

Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399. Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

See Also

nma.pdbs, nma, plot.bio3d, entropy.

Examples

## Not run: 
# ids <- c("1a70_A", "1czp_A", "1frd_A", "1fxi_A", "1iue_A", "1pfd_A")
# raw.files <- get.pdb(ids, path = "raw_pdbs")
# files <- pdbsplit(raw.files, ids, path = "raw_pdbs/split_chain")
# 
# ## Sequence Alignement
# pdbs <- pdbaln(files)
# 
# ## Normal mode analysis on aligned data
# all.modes <- nma.pdbs(pdbs, rm.gaps=TRUE)
# 
# ## Plot fluctuations
# plot.enma(all.modes, pdbs=pdbs, conservation=TRUE)
# 
# ## group and spread fluctuation profiles
# grps <- rep(NA, length(pdbs$id))
# grps[c(2,3)]=1
# grps[c(4,5)]=2
# 
# plot.enma(all.modes, pdbs=pdbs, col=grps, spread=TRUE)
# ## End(Not run)