R for Amplicon-Sequencing-Based Microbial-Ecology

Characterizing environmental microbiota diversity using amplicon-based next generation sequencing (NGS) data. Functions are developed to manipulate operational taxonomic unit (OTU) table, perform descriptive and inferential statistics, and generate publication-quality plots.


News

\name{NEWS} \title{RAM News} \encoding{UTF-8}

\section{Changes in version 1.2.1.3}{

\subsection{GENERAL}{ \itemize{

   \item This is a release that we fixed some bugs.

 }

} % general

\subsection{BUG FIXES}{

\itemize{

 \item Fixed missing link or links in documentation object 'RAM-package.Rd': ‘[ggplot2:ggplot2-package]{ggplot2}’.

 \item Fixed a bug in \code{group.rich}     
}

} % bug fixes } % version 1.2.1.3

\section{Changes in version 1.2.1.2}{

\subsection{GENERAL}{ \itemize{

   \item This is a release that we fixed some bugs.

 }

} % general

\subsection{BUG FIXES}{

\itemize{

 \item Fixed a bug in \code{shared.OTU} where an error occurs 
 when no otus are shared by all samples.

 \item Fixed a bug in \code{shared.Taxa} where an error occurs 
 when no taxa are shared by all samples.

 \item Resolved the conflit between the 'summary.cca' function 
 of 'vegan' and the one of 'ade4'. in an internal function 
 .analysis.helper

 \item Fixed seq_var to work with gridExtra version 2.0.0

}

} % bug fixes } % version 1.2.1.2

\section{Changes in version 1.2.1.1}{

\subsection{GENERAL}{ \itemize{

   \item This is a release that we fixed some bugs.

 }

} % general

\subsection{BUG FIXES}{

\itemize{

 \item Fixed a bug in \code{filter.OTU} for filtering by number
 of sequences per sample.

}

} % bug fixes } % version 1.2.1.1

\section{Changes in version 1.2.1}{

\subsection{GENERAL}{ \itemize{

   \item This is a release with new functions and features. In
   the same we also fix some issues of plot functions.

 }

} % general

\subsection{BUG FIXES}{

\itemize{

 \item Fixed the labels on x axis of plots generated by 
 \code{group.rich} & \code{group.spec}

 \item Fixed a bug in \code{filter.OTU} 

  \item Fixed a bug in \code{tax.abund} substitues spaces in 
   names of the output dataframes with "_".


}

} % bug fixes

\subsection{NEW FUNCTIONS}{ \itemize{

  \item Function \code{phylo_taxonomy} plot hierarchical 
  taxonomic tree with relative abundance of all taxa at a 
  give rank if category variables are provided. Nonsplitting 
  nodes are collapsed as ape::plot.phylo does.

  \item Function \code{phylog_taxonomy} This function plot 
  hierarchical taxonomic tree, the leaves are taxa at a give 
  rank, nonsplitting nodes are not collapsed.

  \item Function \code{factor.abundance} reates a stacked bar
  plot showing the abundance of all classifications at the 
  given taxonomic rank for each level of a metadata category 
  variable.

  \item Function \code{seq_var} new function calculates and 
  plots inter/intra specific variation for an alignment.

  \item Function \code{network_data} new function to generate 
  a list of network nodes and edges based on an otu table and 
  associated metadata

  \item Function \code{group.abundance.meta} an updated version 
  of \code{\link{group.abundance}}, which groups samples by 
  metadata category variables if provided.

}

} % NEW FUNCTIONS

\subsection{NEW DATA}{ \itemize{

 \item DATA \code{alignment} new data for \code{\link{seq_var}.

} % NEW DATA

} % version 1.2.1

\section{Changes in version 1.2.0}{

\subsection{GENERAL}{ \itemize{

   \item This is a release with new functions and features. In
   the same we also fix some issues of plot functions.

 }

} % general

\subsection{BUG FIXES}{

\itemize{

 \item Fixed a bug in Function \code{get.rank} that keeping 
 otus without identified taxon name at a given rank; e.g. 
 'g__' or 'g__;'

}

} % bug fixes

\subsection{NEW FUNCTIONS}{ \itemize{

  \item Function \code{match.data} to match samples in ecology 
  datasets and metadata set. Only samples that present in both 
  will be kept and  reordered to match all datasets.

  \item Function \code{OTU.revamp} returns a list to describe 
  the percent of classifed  otus and sequences at each given 
  taxonomy ranks and visualize  the output in a barplot.

  \item Function \code{transpose.LCA} transpose OTU tables with 
   each OTU being annotated with its LCA.

  \item Function \code{theme_ggplot} provide two ggplot themes 
  RAM.color and R.border for customized fancy plots.

  \item Function \code{combine.OTU} combine otus for the same 
  sample. Suggested  to be use for bacterial 16S datasets. 

  \item Function \code{filter.META} Select METADATA Variables 
  and remove the ones  that only have one level, neither numeric 
  nor factor and /  or with missing data.

  \item Function \code{.valid.data} check whether ecology data 
  sets have same  

  \item Function \code{assist.ado} perform ADONIS Analysis for 
  ecology data sets.  

  \item Function \code{filter.Taxa} filter taxonomic abundance 
  matrices by total  counts or maximum relative abundance.  

  \item Function \code{data.clust} plot hierarchical clusters 
  of samples based on  ecology data set. 

  \item Function \code{META.clust} Plot Hierarchical Cluster 
  Of samples based on  metadata

  \item Function \code{assist.NB} negative binomial test of 
  seleted otuID or  taxon name.

  \item Function \code{envis.NB} plot the negative binomial 
  model for selected  otuID or taxon name.

  \item Function \code{group.rich} Barplot of richness for a 
  given metadata  variable.

  \item Function \code{group.spec} Boxplot of richness for a 
  given metadata  variable.

  \item Function \code{OTU.ord} visualize cca/rda analysis on 
  otus 

  \item Function \code{Taxa.ord} visualize cca/rda analysis on 
  taxa groups at a  given rank.

  \item Function \code{group.Taxa.box} boxplot of taxa 
  distribution among groups.

  \item Function \code{group.Taxa.bar} barplot of taxa 
  distribution among groups.

  \item Function \code{group.abunda.taxa} barplot of selected 
  taxa in each group.

  \item Function \code{group.venn} venn diagrams for taxa 
  shared by different  communities

  \item Function \code{shared.Taxa} summarize taxa shared by 
  all samples

  \item Function \code{valid.taxonomy} check whether the format 
  of the taxonomy  lineages in the otu tables are supported by RAM

  \item Function \code{reformat.taxonomy} reformat the taxonomy  
  lineages in the otu tables that supported by RAM

  \item Function \code{sample.map} plot the number of samples 
  collected from  each location. For plotting distant sampling 
  sites.

  \item Function \code{sample.site} alternative view of RAM 
  functons sample.map and  sample.locations, suitable for plot 
  closely located sampling  sites.

  \item Function \code{group.diversity} plot diversity indices 
  among different  groups.

  \item Function \code{RAM.pal} generate customized color pattern.

}

} % new functions

\subsection{NEW FEATURES}{ \itemize{

  \item Function \code{read.OTU} now can import both "," or 
 "\t" delimited files.

  \item Function \code{read.meta} now can import both "," or 
 "\t" delimited files.

  \item Function \code{OTU.recap} returns a list to describe 
  the percent of classifed otus and sequences at each given 
  taxonomy ranks and visualize the output in a barplot.

  \item Added standardize and dist.method options to Function 
  \code{group.heatmap}.

  \item Function \code{group.abundance} can process more than 
  2 OTU tables now.

  \item Function \code{group.top.number} can process more than 
  2 OTU tables now.

  \item Function \code{group.top.percent} can process more than 
  2 OTU tables now.

  \item Function \code{group.indicators} can process more than 
  2 OTU tables now.

}

} % new features

% \subsection{INSTALLATION AND BUILDING}{ % \itemize{

% \item Function

% \item Function

% } % } % installation and building

\subsection{DEPRECATED}{

\itemize{

  \item Function \code{write.OTU} removed and replaced by 
  \code{write.data} function
  
 }   

} % deprecated

} % version 1.2.0

\section{Changes in version 1.1.0}{

\subsection{GENERAL}{ \itemize{

   \item This is a release with new functions and features. In
   the same we also fix some issues of plot functions.

 }

} % general

\subsection{BUG FIXES}{

\itemize{

 \item Function \code{tax.split} previously used a function 
  \code{splitstackshape::concat.split}, which is deprecated. Replaced 
  with new function in RAM \code{split.col}.  

 \item Function \code{group.indicators} fix the bug caused by previous
  version of tax.split, which call function 
  \code{splitstackshape::concat.split}, which is not required any more.   

  \item Function \code{tax.abund} failed to remove unclassified 
  taxon groups in defined blacklist when drop.unclassified is
  set as TRUE. 

  \item Function \code{group.abundance} needs \code{tax.abund} when 
  plot relative abundance of top taxon groups at each ranks. Now it 
  correctly remove unclassified taxon groups when drop.unclassified 
  option is set TRUE.
  
  \item \code{tax.fill} failed to recognize unclassified 
  taxon groups in defined blacklist and replace them with the OTUs 
  lowest comman ancestor. 

  \item \code{...} 

}

} % bug fixes

\subsection{NEW FUNCTIONS}{ \itemize{

  \item Function \code{OTU.diversity} calculates most used 
  diversity indices for each samples based on OTU tables.

  \item Function \code{core.OTU} summarizes most prevelant otus.

  \item Function \code{core.Taxa} summarizes most prevelant taxon 
  groups.

  \item \code{group.OTU} plot function for the distribution of 
  selected otus.

  \item \code{filter.OTU} function to subset OTUs by either total 
  count or relative abundance.
 
  \item \code{OTU.recap} summarizes classified OTUs at each taxonomic
  ranks.
 
  \item \code{.get.rank.name} internal function to generate the name 
  of a given taxonomic rank.

  \item \code{LCA.OTU} function to obtain LCA for each otu. Unclassified 
  taxa are removed and the lowest rank that an otu can be assigned to is 
  returned. 
  
  \item \code{correlation} plot function to display correlation 
   coefficient (or covariance) among taxa at a give rank and / or 
  numeric variables of metadata. 
        
  \item \code{col.splitup} function to split a column of a data frame by 
  predefined separator.

}

} % new functions

} % version 1.1.0

Reference manual

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