Main OrthoMCL Analysis

Description

Main function for analyzing the statistical association of OG (orthologous group) presence with phenotype data

Usage

AnalyzeOrthoMCL(mcl_data, pheno_data, model, species_name, resp = NULL,
  fix2 = NULL, rndm1 = NULL, rndm2 = NULL, multi = 1, time = NULL,
  event = NULL, time2 = NULL, startnum = 1, stopnum = "end",
  output_dir = NULL, sig_digits = NULL, princ_coord = 0)

Arguments

Value

A matrix with the following columns: OG, p-values, Bonferroni corrected p-values, mean phenotype of OG-containing taxa, mean pheotype of OG-lacking taxa, taxa included in OG, taxa not included in OG

Examples

#Linear Model

## Not run: 
mcl_mtrx <- AnalyzeOrthoMCL(after_ortho_format, pheno_data, 'lm',
 'Treatment', resp='RespVar')

## End(Not run)

# the rest of the examples are not run for time's sake
#Linear Mixed Effect with one random effect
## Not run: 
mcl_mtrx <- AnalyzeOrthoMCL(after_ortho_format, pheno_data, 'lmeR1',
'Treatment', resp='RespVar', rndm1='Experiment')

## End(Not run)


#Linear Mixed Effect with two independent random effects
## Not run: 
mcl_mtrx <- AnalyzeOrthoMCL(after_ortho_format, pheno_data, 'lmeR2ind',
 'Treatment', resp='RespVar', rndm1='Experiment', rndm2='Vial')

## End(Not run)


#Linear Mixed Effect with rndm2 nested in rndm1
## Not run: 
mcl_mtrx <- AnalyzeOrthoMCL(after_ortho_format, pheno_data, 'lmeR2nest',
 'Treatment',  resp='RespVar', rndm1='Experiment', rndm2='Vial')

## End(Not run) 


#Linear Mixed Effect with two independent random effects and one additional fixed effect
## Not run: 
mcl_mtrx3 <- AnalyzeOrthoMCL(after_ortho_format, pheno_data, 'lmeF2',
 'Treatment', resp='RespVar', fix2='Treatment', rndm1='Experiment', rndm2='Vial', princ_coord = 4)

## End(Not run)


#Wilcoxon Test
## Not run: 
mcl_mtrx <- AnalyzeOrthoMCL(after_ortho_format, pheno_data, 'wx',
 'Treatment', resp='RespVar')

## End(Not run)

# ~ 5 minutes
#Survival with two independent random effects, run on multiple cores
## Not run: 
mcl_mtrx <- AnalyzeOrthoMCL(after_ortho_format, starv_pheno_data, 'TRT', model='survmulti',
 time='t2', event='event', rndm1='EXP', rndm2='VIAL', multi=1)

## End(Not run)

# ~ 5 minutes
#Survival with two independent random effects and one additional fixed effect,
#including drops on multi cores
## Not run: 
mcl_mtrx <- AnalyzeOrthoMCL(after_ortho_format, starv_pheno_data, 'TRT', model='survmulticensor',
 time='t1', time2='t2', event='event', rndm1='EXP', rndm2='VIAL', fix2='BACLO', multi=1)
 
## End(Not run)
#to be appended with SurvAppendMatrix

Show Principal Components Breakdown

Description

Function to show Principal Components statistics based on the OrthoMCL presence absence groupings.

Usage

CalculatePrincipalCoordinates(mcl_data)

Arguments

Value

returns a named list of principal components and accompanying proportion of variance for each

Examples

CalculatePrincipalCoordinates(after_ortho_format)

Format file from output of OrthoMCL algorithm before use in AnalyzeOrthoMCL

Description

After running OrthoMCL and/or submitting to www.orthomcl.org, formats the output file to be used in AnalyzeOrthoMCL

Usage

FormatAfterOrtho(file, format = "ortho")

Arguments

Value

a list of matrices; (1) a presence/absence matrix of taxa per OG, (2) a list of the specific protein ids within each OG

Examples

file <- system.file('extdata', 'orthologGroups.txt', package='MAGNAMWAR')
after_ortho_format <- FormatAfterOrtho(file)

file_grps <- system.file('extdata', 'groups_example_r.txt', package='MAGNAMWAR')
after_ortho_format_grps <- FormatAfterOrtho(file_grps, format = 'groups')

Format all raw GenBank fastas to single OrthoMCL compatible fasta file

Description

Creates the composite fasta file for use in running OrthoMCL and/or submitting to www.orthomcl.org

Usage

FormatMCLFastas(fa_dir, genbnk_id = 4)

Arguments

Value

Returns nothing, but prints the path to the final OrthoMCL compatible fasta file

Examples

## Not run: 
dir <- system.file('extdata', 'fasta_dir', package='MAGNAMWAR')
dir <- paste(dir,'/',sep='')
formatted_file <- FormatMCLFastas(dir)

## End(Not run)

Join Representative Sequences

Description

Joins the OrthoMCL output matrix to representative sequences

Usage

JoinRepSeq(mcl_data, fa_dir, mcl_mtrx, fastaformat = "new")

Arguments

Value

Returns the original OrthoMCL output matrix with additional columns: representative sequence taxon, representative sequence id, representative sequence annotation, representative sequence

Examples

## Not run: 
dir <- system.file('extdata', 'fasta_dir', package='MAGNAMWAR')
dir <- paste(dir,'/',sep='')
joined_mtrx_grps <- JoinRepSeq(after_ortho_format_grps, dir, mcl_mtrx_grps, fastaformat = 'old')

## End(Not run)

Manhattan Plot of All Taxa

Description

Manhattan plot that graphs all p-values for taxa.

Usage

ManhatGrp(mcl_data, mcl_mtrx, tree = NULL)

Arguments

Value

a manhattan plot

References

Some sort of reference

Examples

ManhatGrp(after_ortho_format, mcl_mtrx)

#@param equation of line of significance, defaults to -log10((.05)/dim(pdgs)[1])

Plot of a PDG and Data with Standard Error Bars

Description

Bar plot of PDG vs phenotype data with presence of taxa in PDG indicated by color

Usage

PDGPlot(data, mcl_matrix, OG = "NONE", species_colname, data_colname,
  xlab = "Taxa", ylab = "Data", ylimit = NULL, tree = NULL,
  order = NULL, main_title = NULL)

Arguments

Value

a barplot with taxa vs phenotypic data complete with standard error bars

Examples

PDGPlot(pheno_data, mcl_mtrx, 'OG5_126778', 'Treatment', 'RespVar', ylimit=12)

Number of PDGs vs OGs/PDG

Description

Barplot that indicates the number of PDGs vs OGs(clustered orthologous groups) in a PDG

Usage

PDGvOG(mcl_data, num = 40, ...)

Arguments

Value

a barplot with a height determined by the second column and the first column abbreviated to accomodate visual spacing

Examples

PDGvOG(after_ortho_format_grps,2)

Phylogenetic Tree with Attached Bar Plot and Standard Error Bars

Description

Presents data for each taxa including standard error bars next to a phylogenetic tree.

Usage

PhyDataError(phy, data, mcl_matrix, species_colname, data_colname,
  color = NULL, OG = NULL, xlabel = "xlabel", ...)

Arguments

Value

A phylogenetic tree with a barplot of the data (with standard error bars) provided matched by taxa.

References

Some sort of reference

Examples

file <- system.file('extdata', 'muscle_tree2.dnd', package='MAGNAMWAR')
PhyDataError(file, pheno_data, mcl_mtrx, species_colname = 'Treatment', data_colname = 'RespVar',
 OG='OG5_126778', xlabel='TAG Content')

Print OG Sequences

Description

Print all protein sequences and annotations in a given OG

Usage

PrintOGSeqs(after_ortho, OG, fasta_dir, out_dir = NULL, outfile = "none")

Arguments

Value

A fasta file with all protein sequences and ids for a given OG

Examples

## Not run: 
OG <- 'OG5_126968'
dir <- system.file('extdata', 'fasta_dir', package='MAGNAMWAR')
dir <- paste(dir,'/',sep='')

PrintOGSeqs(after_ortho_format, OG, dir)

## End(Not run)

QQPlot

Description

Makes a qqplot of the p-values obtained through AnalyzeOrthoMCL

Usage

QQPlotter(mcl_mtrx)

Arguments

Value

a qqplot of the p-values obtained through AnalyzeOrthoMCL

References

Some sore of reference

Examples

QQPlotter(mcl_mtrx)

Write RAST files to Genbank formats OrthoMCL Analysis

Description

Useful for reformating RAST files to GBK format

Usage

RASTtoGBK(input_fasta, input_reference, out_name_path)

Arguments

Examples

## Not run: 
lfrc_fasta <- system.file('extdata', 'RASTtoGBK//lfrc.fasta', package='MAGNAMWAR')
lfrc_reference <- system.file('extdata', 'RASTtoGBK//lfrc_lookup.csv', package='MAGNAMWAR')
lfrc_path <- system.file('extdata', 'RASTtoGBK//lfrc_out.fasta', package='MAGNAMWAR')

RASTtoGBK(lfrc_fasta,lfrc_reference,lfrc_path)

## End(Not run)

Append Survival Test Outputs

Description

Function used to append all .csv files that are outputted from AnalyzeOrthoMCL into one matrix.

Usage

SurvAppendMatrix(work_dir, out_name = "surv_matrix.csv", out_dir = NULL)

Arguments

Value

A csv file containing a matrix with the following columns: OG, p-values, Bonferroni corrected p-values, mean phenotype of OG-containing taxa, mean pheotype of OG-lacking taxa, taxa included in OG, taxa not included in OG

Examples

## Not run: 
file <- system.file('extdata', 'outputs', package='MAGNAMWAR')
directory <- paste(file, '/', sep = '')
SurvAppendMatrix(directory)

## End(Not run)

Print analyzed matrix

Description

Writes a tab separated version of the analyzed OrthoMCL data with or without the joined representative sequences

Usage

WriteMCL(mtrx, filename)

Arguments

Value

The path to the written file

Examples

## Not run: 
WriteMCL(mcl_mtrx, 'matrix.tsv')
#mcl_mtrx previously derived from AnalyzeOrthoMCL() or join_repset()

## End(Not run)

Formatted output of OrthoMCL.

Description

A list created by inputting the output of OrthoMCL clusters into the FormatAfterOrtho function.

Usage

after_ortho_format

Format

List of 2: (1) presence absence matrix, (2) protein ids:

pa_matrix

matrix showing taxa presence/absence in OG

proteins

matrix listing protein_id contained in each OG

Formatted output of OrthoMCL.

Description

A list created by inputting the output of OrthoMCL clusters into the FormatAfterOrtho function.

Usage

after_ortho_format_grps

Format

List of 2: (1) presence absence matrix, (2) protein ids:

pa_matrix

matrix showing taxa presence/absence in OG

proteins

matrix listing protein_id contained in each OG

Final output of join_repset.

Description

A data frame containing the final results of statistical analysis with protein ids, annotations, and sequences added.

Usage

joined_mtrx

Format

A data frame with 17 rows and 11 variables:

OG

taxa cluster id, as defined by OrthoMCL

pval1

p-value, based on presence absence

corrected_pval1

Bonferroni p-value, corrected by number of tests

mean_OGContain

mean of all taxa phenotypes in that OG

mean_OGLack

mean of all taxa phenotypes not in that OG

taxa_contain

taxa in that cluster

taxa_miss

taxa not in that cluster

rep_taxon

randomly selected representative taxa from the cluster

rep_id

protein id, from randomly selected representative taxa

rep_annot

fasta annotation, from randomly selected representative taxa

rep_seq

AA sequence, from randomly selected representative taxa

Final output of join_repset.

Description

A data frame containing the final results of statistical analysis with protein ids, annotations, and sequences added.

Usage

joined_mtrx_grps

Format

A data frame with 10 rows and 11 variables:

OG

taxa cluster id, as defined by OrthoMCL

pval1

p-value, based on presence absence

corrected_pval1

Bonferroni p-value, corrected by number of tests

mean_OGContain

mean of all taxa phenotypes in that OG

mean_OGLack

mean of all taxa phenotypes not in that OG

taxa_contain

taxa in that cluster

taxa_miss

taxa not in that cluster

rep_taxon

randomly selected representative taxa from the cluster

rep_id

protein id, from randomly selected representative taxa

rep_annot

fasta annotation, from randomly selected representative taxa

rep_seq

AA sequence, from randomly selected representative taxa

Final output of AnalyzeOrthoMCL

Description

A matrix containing the final results of statistical analysis.

Usage

mcl_mtrx

Format

A matrix with 17 rows and 7 variables:

OG

taxa cluster id, as defined by OrthoMCL

pval1

p-value, based on presence absence

corrected_pval1

Bonferroni p-value, corrected by number of tests

mean_OGContain

mean of all taxa phenotypes in that OG

mean_OGLack

mean of all taxa phenotypes not in that OG

taxa_contain

taxa in that cluster

taxa_miss

taxa not in that cluster

Final output of AnalyzeOrthoMCL

Description

A matrix containing the final results of statistical analysis.

Usage

mcl_mtrx_grps

Format

A matrix with 10 rows and 7 variables:

OG

taxa cluster id, as defined by OrthoMCL

pval1

p-value, based on presence absence

corrected_pval1

Bonferroni p-value, corrected by number of tests

mean_OGContain

mean of all taxa phenotypes in that OG

mean_OGLack

mean of all taxa phenotypes not in that OG

taxa_contain

taxa in that cluster

taxa_miss

taxa not in that cluster

Triglyceride (TAG) content of fruit flies dataset.

Description

A subset of the TAG content of fruit flies, collected in the Chaston Lab, to be used as a brief example for tests in AnalyzeOrthoMCL.

Usage

pheno_data

Format

A data frame with 586 rows and 4 variables:

Treatment

4-letter taxa designation of associated bacteria

RespVar

response variable, TAG content

Vial

random effect variable, vial number of flies

Experiment

random effect variable, experiment number of flies

Starvation rate of fruit flies dataset.

Description

A subset of the Starvation rate of fruit flies, collected in the Chaston Lab, to be used as a brief example for survival tests in AnalyzeOrthoMCL.

Usage

starv_pheno_data

Format

A matrix with 543 rows and 7 variables:

EXP

random effect variable, experiment number of flies

VIAL

random effect variable, vial number of flies

BACLO

fixed effect variable, loss of bacteria in flies

TRT

4-letter taxa designation of associated bacteria

t1

time 1

t2

time 2

event

event