Last data update: 2014.03.03
R: DSSP summary plot for secondary structure elements (proteins)
dssp_summary R Documentation
DSSP summary plot for secondary structure elements (proteins)
Description
Plots summary plot for secondary structure motifs based on the output of the widely used classification program DSSP, which takes hydrogen bonds into account. The default order is: "3-Helix", "4-Helix", "5-Helix", "Bend", "Beta-Bridge", "Beta-Strand", "Turn".
Usage
dssp_summary( dsspData,
printLegend = FALSE,
useOwnLegend = FALSE,
elementNames = NA,
colours = NA,
showValues = NA,
showResidues = NA,
plotType = "dots",
selectedElements = NA,
barePlot = FALSE,
... )
Arguments
dsspData
Table containing the information on the secondary structure motifs.
printLegend
If TRUE, a legend is printed on the right hand side of the plot.
useOwnLegend
If FALSE, the names of the secondary structure elements are considered to be in default order.
elementNames
Vector of names for the secondary structure elements.
colours
A vector of colours, that can be specified to replace the default ones.
showValues
A vector of boundaries for the values (two elements).
showResidues
A vector of boundaries for the residues (two elements).
plotType
Either "dots", "curves" or "bars".
selectedElements
A vector of names of the elements selected for plotting.
barePlot
Boolean, indicating whether the plot is to be made without any additional information.
...
Additional arguments (ellipsis).
Author(s)
Christian Margreitter
Examples
# see "extdata/dssp_summary_example.txt.gz" for format information
dssp_summary( load_dssp_summary( system.file( "extdata/dssp_summary_example.txt.gz",
package = "MDplot" ) ) )
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(MDplot)
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
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MDplot/dssp_summary.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dssp_summary
> ### Title: DSSP summary plot for secondary structure elements (proteins)
> ### Aliases: dssp_summary
> ### Keywords: dssp
>
> ### ** Examples
>
> # see "extdata/dssp_summary_example.txt.gz" for format information
> dssp_summary( load_dssp_summary( system.file( "extdata/dssp_summary_example.txt.gz",
+ package = "MDplot" ) ) )
3-Helix 4-Helix 5-Helix Turn B-Strand B-Bridge Bend
[1,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[2,] 0.0 0.0 0.0 0.0 0.0 0.3 0.0
[3,] 0.0 0.0 0.0 0.0 0.0 0.0 1.7
[4,] 0.0 0.0 0.0 0.0 0.0 37.1 4.5
[5,] 0.0 0.0 0.0 0.0 0.0 0.0 4.3
[6,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[7,] 0.0 0.0 0.0 0.0 97.6 0.0 0.0
[8,] 0.0 0.0 0.0 0.0 99.8 0.0 0.0
[9,] 0.0 0.0 0.0 0.0 99.9 0.0 0.0
[10,] 0.0 0.0 0.0 0.0 92.3 0.0 0.0
[11,] 0.0 0.0 0.0 0.0 69.5 0.0 0.0
[12,] 0.0 0.0 0.0 0.0 0.0 0.0 0.1
[13,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[14,] 0.0 0.0 0.0 98.8 0.0 0.0 0.0
[15,] 2.4 79.6 0.0 2.3 0.0 0.0 15.8
[16,] 4.3 79.8 0.0 14.8 0.0 0.0 1.1
[17,] 16.1 79.8 0.0 1.0 0.0 0.0 3.1
[18,] 15.6 79.8 0.0 0.0 0.0 0.0 4.5
[19,] 20.7 43.5 0.0 0.0 0.0 0.0 35.6
[20,] 0.0 0.0 0.0 0.5 0.0 0.0 99.1
[21,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[22,] 0.0 0.0 0.0 0.0 87.8 4.1 6.7
[23,] 0.0 0.0 0.0 0.0 95.0 0.0 0.0
[24,] 0.0 0.0 0.0 0.0 95.4 0.0 0.0
[25,] 0.0 0.0 0.0 0.0 99.8 0.0 0.0
[26,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[27,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[28,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[29,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[30,] 0.0 0.0 0.0 0.0 99.3 0.0 0.0
[31,] 0.0 0.0 0.0 0.0 0.0 0.0 71.5
[32,] 0.0 0.0 0.0 0.0 9.9 48.6 0.0
[33,] 0.0 0.0 0.0 0.0 9.9 0.6 84.9
[34,] 0.0 0.0 0.0 4.5 0.0 0.0 94.7
[35,] 0.0 0.0 0.0 0.0 0.0 0.0 95.9
[36,] 0.0 0.0 0.0 0.0 0.0 0.0 0.6
[37,] 0.0 0.0 0.0 0.0 0.5 0.0 0.0
[38,] 0.0 0.0 0.0 0.0 96.8 3.0 0.0
[39,] 0.0 0.0 0.0 0.0 96.9 0.0 0.0
[40,] 0.0 0.0 0.0 0.0 85.5 0.0 0.0
[41,] 0.0 0.0 0.0 0.0 88.1 0.0 0.0
[42,] 0.0 0.0 0.0 0.0 97.2 2.6 0.0
[43,] 0.0 0.0 0.0 5.4 51.9 0.1 2.5
[44,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[45,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[46,] 0.0 0.0 0.0 0.0 35.7 0.9 23.0
[47,] 0.0 0.0 0.0 0.0 36.9 6.2 0.0
[48,] 0.0 0.0 0.0 0.5 11.6 8.8 0.0
[49,] 0.0 0.0 0.0 0.1 0.0 0.0 22.8
[50,] 0.0 0.0 0.0 0.0 0.0 0.0 4.9
[51,] 0.0 0.0 0.0 0.0 72.6 3.7 0.0
[52,] 0.0 0.0 0.0 0.0 87.9 0.3 0.0
[53,] 0.0 0.0 0.0 0.0 85.4 5.6 0.0
[54,] 0.0 0.0 0.0 0.0 6.1 0.1 0.0
[55,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[56,] 0.0 0.0 0.0 0.0 0.1 0.0 0.4
[57,] 0.0 0.0 0.0 0.0 98.1 1.0 0.0
[58,] 0.0 0.0 0.0 0.0 98.2 0.8 0.0
[59,] 0.0 0.0 0.0 83.4 5.0 0.2 0.0
[60,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[61,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[62,] 0.0 0.0 0.0 0.0 0.0 0.4 99.4
[63,] 0.0 0.0 0.0 0.0 4.8 0.0 14.3
[64,] 0.0 0.0 0.0 0.0 99.4 0.3 0.0
[65,] 0.0 0.0 0.0 0.0 99.7 0.0 0.0
[66,] 0.0 0.0 0.0 0.0 99.8 0.0 0.0
[67,] 0.0 0.0 0.0 0.0 99.9 0.0 0.0
[68,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[69,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[70,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[71,] 0.0 0.0 0.0 0.0 95.4 0.0 0.0
[72,] 0.0 0.0 0.0 0.0 95.0 0.0 0.0
[73,] 0.0 0.0 0.0 6.7 87.8 4.1 0.0
[74,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[75,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[76,] 0.0 0.0 0.0 99.8 0.0 0.0 0.1
[77,] 0.1 99.3 0.0 0.3 0.0 0.0 0.3
[78,] 0.0 99.7 0.0 0.3 0.0 0.0 0.0
[79,] 0.0 99.9 0.0 0.0 0.0 0.0 0.0
[80,] 0.0 100.0 0.0 0.0 0.0 0.0 0.0
[81,] 0.1 99.9 0.0 0.1 0.0 0.0 0.0
[82,] 0.4 99.0 0.0 0.2 0.0 0.0 0.5
[83,] 1.7 95.5 0.0 0.0 0.0 0.0 2.8
[84,] 3.4 52.1 0.1 0.0 0.0 0.0 44.4
[85,] 0.0 0.8 0.5 0.0 0.0 0.0 90.4
[86,] 0.0 0.0 0.0 0.0 0.0 0.0 27.3
[87,] 0.0 0.0 0.0 0.0 0.1 0.0 0.0
[88,] 0.0 0.0 0.0 0.0 25.8 0.0 0.0
[89,] 0.0 0.0 0.0 0.0 96.5 3.5 0.0
[90,] 0.0 0.0 0.0 0.0 96.0 0.0 0.0
[91,] 0.0 0.0 0.0 0.0 96.1 0.0 0.0
[92,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[93,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[94,] 0.0 0.0 0.0 76.9 0.5 0.0 0.0
[95,] 0.0 0.0 0.0 0.2 0.0 0.0 99.8
[96,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[97,] 0.0 0.0 0.0 66.4 0.0 27.0 6.2
[98,] 16.6 0.0 0.0 0.9 0.0 0.0 82.5
[99,] 16.7 0.0 0.0 0.0 0.0 0.0 83.3
[100,] 16.7 0.0 0.0 0.0 0.1 0.0 83.1
[101,] 0.0 0.0 0.0 0.0 92.9 1.1 1.9
[102,] 0.0 0.0 0.0 0.0 98.3 0.5 0.0
[103,] 0.0 0.0 0.0 0.0 80.9 0.0 0.0
[104,] 0.0 0.0 0.0 0.0 81.0 0.0 0.0
[105,] 0.0 0.0 0.0 0.0 80.6 18.6 0.0
[106,] 0.0 0.0 0.0 0.0 10.1 0.0 1.6
[107,] 0.0 0.0 0.0 0.0 0.1 0.0 0.0
[108,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0
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> dev.off()
null device
1
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providing 
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