lmPlot: Draw a comprehensive LowMACA plot

In LowMACA: LowMACA - Low frequency Mutation Analysis via Consensus Alignment

Description

LowMACA comprehensive plot is a four layers plot that summarize the entire LowMACA output

Usage

lmPlot(object , conservation=NULL, splitLen=NULL)

Arguments

object	a LowMACA class object
conservation	a numeric value in the range of 0-1 that defines the threshold of trident conservation score to include the specified position. The default value is inherited from the slot entropy, whose default is 0.1
splitLen	An integer, defines after how many amino acids the plot should be split By default this parameter is set to NULL, that mean that the plot is not split.

Details

The method returns a plot, which is divided into four layers. The LowMACA object must have been passed through the methods alignSequences , getMutations , mapMutations and entropy. The four layers of the plot are:

1. The bar plot visualized by bpAll

2. The distribution of mutations against the 95% confidence interval superior limit of the null hypothesis (dotted line) with orange bars representing a position with a pvalue <0.05 and a red star for qvalue<0.05

3. The Trident score distribution

4. The logo plot representing the consensus sequence

If this plot is used on a LowMACA object with a single protein, the result is formed by three layers only:

1. The bar plot visualized by bpAll

2. The Pfam domains structure inside the protein

3. The distribution of mutations against the 95% confidence interval superior limit of the null hypothesis (dotted line) with orange bars representing a position with a pvalue <0.05 and a red star for qvalue<0.05

Value

NULL

Author(s)

Stefano de Pretis , Giorgio Melloni

See Also

alignSequences getMutations mapMutations entropy bpAll

Examples

#Load homeobox example and draw the plot
data(lmObj)
#Calculate statistics for nullProfile
lmObj <- entropy(lmObj)
lmPlot(lmObj)

Example output

Checking if clustalo is in the PATH...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
sh: 1: /usr/bin/perl: Permission denied
sh: 1: /usr/bin/perl: Permission denied
Warning messages:
1: In .ClustalChecks(ClustalCommand = "clustalo") :
  Clustal Omega is not in the PATH:
You can either change clustalo command using lmParams function or use the web service. See ?setup
2: In system(paste(perl, "-MXML::Simple -e 1"), intern = TRUE) :
  running command '/usr/bin/perl -MXML::Simple -e 1' had status 126
3: In .PerlModuleChecks(stop = FALSE, perl = "perl") :
  XML::Simple module for perl is not installed. 
            If you don't want to install a local clustal omega and use the web service, XML::Simple is required

4: In system(paste(perl, "-MLWP -e 1"), intern = TRUE) :
  running command '/usr/bin/perl -MLWP -e 1' had status 126
5: In .PerlModuleChecks(stop = FALSE, perl = "perl") :
  LWP module for perl is not installed. 
            If you don't want to install a local clustal omega and use the web service, LWP is required

Making uniform model...
Assigned bandwidth: 0

LowMACA documentation built on Nov. 8, 2020, 8:14 p.m.