bpAll: Draw a mutation barplot

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

Description

bpAll draws a stacked barplot of the mutations mapped on the consensus sequence

Usage

bpAll(object)

Arguments

object

an object of class LowMACA

Details

Returns a barplot in which mutations are stacked per position on the consensus sequence. Every color represent mutations taht map on the same input sequence (either a protein or a pfam) The LowMACA object must pass through the methods alignSequences , getMutations , mapMutations

Value

NULL

Author(s)

Stefano de Pretis , Giorgio Melloni

See Also

lmPlot

Examples

#Load homeobox example and draw plot
data(lmObj)
lmObj <- entropy(lmObj)
bpAll(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.