Package index • MolEvolvR

All functions

BinaryDomainNetwork(): Domain Network

DownloadAssemblySummary(): Download the combined assembly summaries of genbank and refseq

GCA2lin(): Function to map GCA_ID to TaxID, and TaxID to Lineage

GenContextNetwork(): Genomic Context Directed Network

LineagePlot(): LineagePlot

RepresentativeAccNums(): Function to generate a vector of one Accession number per distinct observation from 'reduced' column

acc2fa(): acc2fa converts protein accession numbers to a fasta format.

acc2lin(): acc2lin

add_leaves(): Adding Leaves to an alignment file w/ accessions

add_lins(): Add Lineages

add_name(): Add Name

add_tax(): add_tax

advanced_opts2est_walltime(): Given MolEvolvR advanced options and number of inputs, calculate the total estimated walltime for the job

alignFasta(): Perform a Multiple Sequence Alignment on a FASTA file.

assert_count_df(): assert_count_df

assign_job_queue(): Decision function to assign job queue

clean_clust_file(): Clean Cluster File

clean_string(): Clean String

cleanup_GeneDesc(): Cleanup GeneDesc

cleanup_clust(): Cleanup Clust

cleanup_domarch(): Cleanup DomArch

cleanup_fasta_header(): Cleanup FASTA Header

cleanup_gencontext(): Cleanup Genomic Contexts

cleanup_lineage(): Cleanup Lineage

cleanup_species(): Cleanup Species

combine_files(): Download the combined assembly summaries of genbank and refseq

combine_full(): Combining full_analysis files

combine_ipr(): Combining clean ipr files

convert_aln2fa(): Adding Leaves to an alignment file w/ accessions

convert_fa2tre(): convert_fa2tre

count_bycol(): Count Bycol

count_to_sunburst() count_to_treemap(): Create an interactive plotly from count data

create_all_col_params(): create_all_col_params

create_lineage_lookup(): Create a look up table that goes from TaxID, to Lineage

create_one_col_params(): create_one_col_params

df_iprscan_domains2fasta(): Using the table returned from make_df_iprscan_domains, construct a domain fasta for a single accession number in the original fasta (i.e., the original fasta argument to make_df_iprscan_domains())

domain_network(): Domain Network

efetch_ipg(): efetch_ipg

elements2words(): Elements 2 Words

exec_interproscan(): exec_interproscan

fasta2fasta_domain(): fasta2fasta_domain

filter_by_doms(): Filter by Domains

filter_freq(): Filter Frequency

find_paralogs(): Find Paralogs

find_top_acc(): Group by lineage + DA then take top 20

format_job_args(): Format job arguments into html-formatted key/value pairs, for including in an email

gc_undirected_network(): Domain Network

generate_all_aln2fa(): Adding Leaves to an alignment file w/ accessions

generate_fa2tre(): generate_fa2tre

generate_msa(): Function to generate MSA using kalign

generate_trees(): generate_trees

get_accnums_from_fasta_file(): Get accnums from fasta file

get_df_ipr_col_names(): Constructor function for interproscan column names (based upon the global variable written in molevol_scripts/R/colnames_molevol.R)

get_df_ipr_col_types(): construct column types for reading interproscan output TSVs (based upon the global variable written in molevol_scripts/R/colnames_molevol.R)

get_job_message(): Produces a mail message that can be sent to a user when their job is accepted. Used by the send_job_status_email() method.

get_proc_medians(): Scrape MolEvolvR logs and calculate median processes

get_proc_weights(): Quickly get the runtime weights for MolEvolvR backend processes

ipg2lin(): ipg2lin

ipr2viz(): IPR2Viz

ipr2viz_web(): IPR2Viz Web

lineage.DA.plot(): Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages

lineage.Query.plot(): Lineage Plot: Heatmap of Queries vs Lineages

lineage.domain_repeats.plot(): Lineage Domain Repeats Plot

lineage.neighbors.plot(): Lineage Plot for top neighbors

lineage_sunburst(): Lineage Sunburst

make_accnums_unique(): make accnums unique

make_df_iprscan_domains(): For a given accession number, get the domain sequences using a interproscan output table & the original FASTA file

make_job_results_url(): Given a pin_id, returns the URL where the user can check the status of their job

make_opts2procs(): Construct list where names (MolEvolvR advanced options) point to processes

map_acc2name(): Default rename_fasta() replacement function. Maps an accession number to its name

map_advanced_opts2procs(): Use MolEvolvR advanced options to get associated processes

msa_pdf(): Multiple Sequence Alignment

pick_longer_duplicate(): Pick Longer Duplicate

plot_estimated_walltimes(): Plot the estimated runtimes for different advanced options and number of inputs

prot2tax(): prot2tax

prot2tax_old(): prot2tax_old

read_iprscan_tsv(): Read an interproscan output TSV with standardized column names and types

remove_astrk(): Remove Astrk

remove_empty(): Remove Empty

remove_tails(): Remove Tails

rename_fasta(): Rename the labels of fasta files

repeat2s(): repeat2s

replaceQMs(): Replace QMs

reveql(): reveql

reverse_operon(): reverse_operon

run_deltablast(): Run DELTABLAST to find homologs for proteins of interest

run_rpsblast(): Run RPSBLAST to generate domain architectures for proteins of interest

send_job_status_email(): Sends a "job accepted" email to a user when their job is accepted, including details about the job submission and how to check its status.

shorten_lineage(): Shorten Lineage

sink.reset(): Sink Reset

stacked_lin_plot(): Stacked Lineage Plot

string2accnum(): string2accnum

summ.DA(): summ.DA

summ.DA.byLin(): summ.DA.byLin

summ.GC(): summ.GC

summ.GC.byDALin(): summ.GC.byDALin

summ.GC.byLin(): summ.GC.byLin

summarize_bylin(): Summarize by Lineage

theme_genes2(): Theme Genes2

to_titlecase(): Changing case to 'Title Case'

total_counts(): Total Counts

upset.plot(): UpSet Plot

wordcloud2_element(): Wordclouds for the predominant domains, domain architectures.

wordcloud3(): Wordcloud3

wordcloud_element(): Wordclouds for the predominant domains, domain architectures

words2wc(): Words 2 Word Counts

write.MsaAAMultipleAlignment(): Write MsaAAMultpleAlignment Objects as algined fasta sequence

write_proc_medians_table(): Write a table of 2 columns: 1) process and 2) median seconds

write_proc_medians_yml(): Compute median process runtimes, then write a YAML list of the processes and their median runtimes in seconds to the path specified by 'filepath'.