noe: Plot NOE violations

In MDplot: Visualising Molecular Dynamics Analyses

Description

This function plots Nuclear-Overhauser-Effect (NOE) violations. Note, that negative violations are not considered, in case they are part of the input.

Usage

noe( noeData,
     printPercentages = TRUE,
     colours = NA,
     lineTypes = NA,
     names = NA,
     plotSumCurves = TRUE,
     maxYAxis = NA,
     printLegend = FALSE,
     ... )

Arguments

noeData	Input matrix. Can be generated by using function load_noe().
printPercentages	If TRUE, the violations will be reported in a relative manner (percent) instead absolute numbers.
colours	Vector of colours to be used for the bars.
lineTypes	If plotSumCurves is TRUE, this vector might be used to specify the types of curves plotted.
names	Vector to name the input columns (legend).
plotSumCurves	If TRUE, the violations are summed up from left to right to show the overall behaviour.
maxYAxis	Can be used to manually set the y-axis of the plot.
printLegend	Boolean, which triggers plotting of the legend.
...	Additional arguments (ellipsis).

Value

Returns a matrix, in which the first column holds the bin boundaries used and the following columns represent either the percentage or absolute numbers of the violations per bin, depending on the specification.

Author(s)

Christian Margreitter

Examples

# GROMOS
noe( load_noe( c( system.file( "extdata/noe_example_1.txt.gz",
                               package = "MDplot" ),
                  system.file( "extdata/noe_example_2.txt.gz",
                               package = "MDplot" ) ) ),
     names = c( "run1", "run2" ), printLegend = TRUE )

Example output

Loading required package: MASS
Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: gtools
       [,1]  [,2]  [,3]
 [1,] 0.025 8.773 9.018
 [2,] 0.075 4.172 4.601
 [3,] 0.125 2.393 1.779
 [4,] 0.175 1.656 1.043
 [5,] 0.225 1.104 1.104
 [6,] 0.275 0.613 0.307
 [7,] 0.325 0.675 0.368
 [8,] 0.375 0.123 0.307
 [9,] 0.425 0.123 0.123
[10,] 0.475 0.123 0.123
[11,] 0.525 0.000 0.000
[12,] 0.575 0.000 0.061
[13,] 0.625 0.000 0.061

MDplot documentation built on May 2, 2019, 7:02 a.m.