From 481450bc97670d57d5bc5e93f7673ae96c5536c1 Mon Sep 17 00:00:00 2001 From: the-mayer <32186106+the-mayer@users.noreply.github.com> Date: Tue, 8 Oct 2024 16:28:34 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20JRaviLab?= =?UTF-8?q?/MolEvolvR@1c22709c7b964915465560dc522eeaacccf2ef33=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- pkgdown.yml | 2 +- reference/GCA2Lineage.html | 100 ++++++++++++++++++++++++ reference/IPG2Lineage.html | 2 +- reference/acc2Lineage.html | 2 +- reference/addLineage.html | 102 +++++++++++++++++++++++++ reference/addTaxID.html | 72 +++++++++++++++++ reference/downloadAssemblySummary.html | 83 ++++++++++++++++++++ reference/index.html | 42 +++++----- reference/plotSunburst.html | 8 +- reference/proteinAcc2TaxID.html | 72 +++++++++++++++++ reference/proteinAcc2TaxID_old.html | 88 +++++++++++++++++++++ search.json | 2 +- sitemap.xml | 12 +-- 13 files changed, 552 insertions(+), 35 deletions(-) create mode 100644 reference/GCA2Lineage.html create mode 100644 reference/addLineage.html create mode 100644 reference/addTaxID.html create mode 100644 reference/downloadAssemblySummary.html create mode 100644 reference/proteinAcc2TaxID.html create mode 100644 reference/proteinAcc2TaxID_old.html diff --git a/pkgdown.yml b/pkgdown.yml index 3a30ba3f..e9b39b15 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 3.1.11 pkgdown: 2.1.1 pkgdown_sha: ~ articles: {} -last_built: 2024-10-08T15:56Z +last_built: 2024-10-08T16:28Z urls: reference: https://jravilab.github.io/MolEvolvR/reference article: https://jravilab.github.io/MolEvolvR/articles diff --git a/reference/GCA2Lineage.html b/reference/GCA2Lineage.html new file mode 100644 index 00000000..a3fe8deb --- /dev/null +++ b/reference/GCA2Lineage.html @@ -0,0 +1,100 @@ + +Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2Lineage • MolEvolvR + Skip to contents + + +
+
+
+ +

Function to map GCA_ID to TaxID, and TaxID to Lineage

+ Source: R/lineage.R +
GCA2Lineage.Rd
+
+ +
+

Function to map GCA_ID to TaxID, and TaxID to Lineage

+
+ +
+

Usage

+ 
GCA2Lineage(
+  prot_data,
+  assembly_path = "/data/research/jravilab/common_data/assembly_summary_genbank.txt",
+  lineagelookup_path = "/data/research/jravilab/common_data/lineage_lookup.tsv",
+  acc_col = "AccNum"
+)
+
+ +
+

Arguments

+ + +
prot_data
+

Dataframe containing a column GCA_ID

+ + +
assembly_path
+

String of the path to the assembly_summary path +This file can be generated using the "downloadAssemblySummary()" function

+ + +
lineagelookup_path
+

String of the path to the lineage lookup file +(taxid to lineage mapping). This file can be generated using the +"create_lineage_lookup()" function

+ + +
acc_col
+
+ +
+
+

Note

+

Currently configured to have at most kingdom and phylum

+
+
+

Author

+

Samuel Chen, Janani Ravi

+
+ +
+ + +
+ + + + + + + diff --git a/reference/IPG2Lineage.html b/reference/IPG2Lineage.html index a200faa1..bb9e67ba 100644 --- a/reference/IPG2Lineage.html +++ b/reference/IPG2Lineage.html @@ -83,7 +83,7 @@

Argumentsassembly_path

String of the path to the assembly_summary path -This file can be generated using the "DownloadAssemblySummary()" function

+This file can be generated using the downloadAssemblySummary function

diff --git a/reference/acc2Lineage.html b/reference/acc2Lineage.html index c4eec71c..deb70cbb 100644 --- a/reference/acc2Lineage.html +++ b/reference/acc2Lineage.html @@ -77,7 +77,7 @@

Argumentsassembly_path

String of the path to the assembly_summary path -This file can be generated using the "DownloadAssemblySummary()" function

+This file can be generated using the "downloadAssemblySummary()" function

lineagelookup_path
diff --git a/reference/addLineage.html b/reference/addLineage.html new file mode 100644 index 00000000..58703cba --- /dev/null +++ b/reference/addLineage.html @@ -0,0 +1,102 @@ + +addLineage — addLineage • MolEvolvR + Skip to contents + + +
+
+
+ +

addLineage

+ Source: R/acc2lin.R, R/lineage.R +
addLineage.Rd
+
+ +
+

addLineage

+

addLineage

+
+ +
+

Usage

+ 
addLineage(
+  df,
+  acc_col = "AccNum",
+  assembly_path,
+  lineagelookup_path,
+  ipgout_path = NULL,
+  plan = "multicore"
+)
+
+addLineage(
+  df,
+  acc_col = "AccNum",
+  assembly_path,
+  lineagelookup_path,
+  ipgout_path = NULL,
+  plan = "multicore"
+)
+
+ +
+

Arguments

+ + +
plan
+
+ +
+
+

Value

+

Describe return, in detail

+
+ +
+

Examples

+ 
if (FALSE) { # \dontrun{
+addLineage()
+} # }
+
+
+
+ + +
+

Developed by Janani Ravi, David Mayer, Evan Brenner, Faisal Alquaddoomi.

+
+ +
+

Site built with pkgdown 2.1.1.

+
+ +
+ + + + + + + diff --git a/reference/addTaxID.html b/reference/addTaxID.html new file mode 100644 index 00000000..3d554a40 --- /dev/null +++ b/reference/addTaxID.html @@ -0,0 +1,72 @@ + +addTaxID — addTaxID • MolEvolvR + Skip to contents + + +
+
+
+ +

addTaxID

+ Source: R/lineage.R +
addTaxID.Rd
+
+ +
+

addTaxID

+
+ +
+

Usage

+ 
addTaxID(data, acc_col = "AccNum", version = T)
+
+ +
+

Arguments

+ + +
version
+
+ +
+ +
+ + +
+

Developed by Janani Ravi, David Mayer, Evan Brenner, Faisal Alquaddoomi.

+
+ +
+

Site built with pkgdown 2.1.1.

+
+ +
+ + + + + + + diff --git a/reference/downloadAssemblySummary.html b/reference/downloadAssemblySummary.html new file mode 100644 index 00000000..5ec705bd --- /dev/null +++ b/reference/downloadAssemblySummary.html @@ -0,0 +1,83 @@ + +Download the combined assembly summaries of genbank and refseq — downloadAssemblySummary • MolEvolvR + Skip to contents + + +
+
+
+ +

Download the combined assembly summaries of genbank and refseq

+ Source: R/lineage.R +
downloadAssemblySummary.Rd
+
+ +
+

Download the combined assembly summaries of genbank and refseq

+
+ +
+

Usage

+ 
downloadAssemblySummary(
+  outpath,
+  keep = c("assembly_accession", "taxid", "species_taxid", "organism_name")
+)
+
+ +
+

Arguments

+ + +
outpath
+

String of path where the assembly summary file should be written

+ + +
keep
+

Character vector containing which columns should be retained and downloaded

+ +
+
+

Author

+

Samuel Chen, Janani Ravi

+
+ +
+ + +
+

Developed by Janani Ravi, David Mayer, Evan Brenner, Faisal Alquaddoomi.

+
+ +
+

Site built with pkgdown 2.1.1.

+
+ +
+ + + + + + + diff --git a/reference/index.html b/reference/index.html index e2d8d3ca..e7f40b80 100644 --- a/reference/index.html +++ b/reference/index.html @@ -49,13 +49,7 @@

All functionsDownloadAssemblySummary() - - -
Download the combined assembly summaries of genbank and refseq
-
- - GCA2lin() + GCA2Lineage()
Function to map GCA_ID to TaxID, and TaxID to Lineage
@@ -97,34 +91,34 @@

All functionsaddName() + addLineage() -
Add Name
+
addLineage

- add_leaves() + addName()
-
Adding Leaves to an alignment file w/ accessions
+
Add Name
- add_name() + addTaxID()
-
Title
+
addTaxID
- add_tax() + add_leaves()
-
add_tax
+
Adding Leaves to an alignment file w/ accessions
- addLineage() + add_name()
-
addLineage
+
Title
advanced_opts2est_walltime() @@ -301,6 +295,12 @@

All functionsdownloadAssemblySummary() + +

+
Download the combined assembly summaries of genbank and refseq
+
+ efetchIPG()
@@ -541,16 +541,16 @@

All functionsprot2tax() + proteinAcc2TaxID() -
prot2tax
+
proteinAcc2TaxID

- prot2tax_old() + proteinAcc2TaxID_old()
-
prot2tax_old
+
proteinAcc2TaxID_old
readIPRScanTSV() diff --git a/reference/plotSunburst.html b/reference/plotSunburst.html index d50da291..4f09476b 100644 --- a/reference/plotSunburst.html +++ b/reference/plotSunburst.html @@ -85,21 +85,21 @@

Examples# sunburst plot plotSunburst(starwars_count)
- + # fill by group size plotSunburst(starwars_count, fill_by_n = TRUE)
- + # treemap plot, ordered by group size plotTreemap(starwars_count, sort_by_n = TRUE)
- + # display al charchaters by homeworld starwars %>% count(homeworld, name) %>% plotTreemap(sort_by_n = TRUE)
- +