diff --git a/pkgdown.yml b/pkgdown.yml index f881804a..97bfe4a2 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 3.1.11 pkgdown: 2.1.1 pkgdown_sha: ~ articles: {} -last_built: 2024-10-07T22:00Z +last_built: 2024-10-08T14:19Z urls: reference: https://jravilab.github.io/MolEvolvR/reference article: https://jravilab.github.io/MolEvolvR/articles diff --git a/reference/IPG2Lineage.html b/reference/IPG2Lineage.html new file mode 100644 index 00000000..a200faa1 --- /dev/null +++ b/reference/IPG2Lineage.html @@ -0,0 +1,125 @@ + +IPG2Lineage — IPG2Lineage • MolEvolvR + Skip to contents + + +
+
+
+ +

IPG2Lineage

+ Source: R/acc2lin.R, R/lineage.R +
IPG2Lineage.Rd
+
+ +
+

Takes the resulting file of an efetch run on the ipg database and

+

Takes the resulting file of an efetch run on the ipg database and +append lineage, and taxid columns

+
+ +
+

Usage

+ 
IPG2Lineage(
+  accessions,
+  ipg_file,
+  refseq_assembly_path,
+  genbank_assembly_path,
+  lineagelookup_path
+)
+
+IPG2Lineage(
+  accessions,
+  ipg_file,
+  refseq_assembly_path,
+  genbank_assembly_path,
+  lineagelookup_path
+)
+
+ +
+

Arguments

+ + +
accessions
+

Character vector of protein accessions

+ + +
ipg_file
+

Path to the file containing results of an efetch run on the +ipg database. The protein accession in 'accessions' should be contained in this +file

+ + +
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

+ + +
assembly_path
+

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

+ +
+
+

Value

+

Describe return, in detail

+
+
+

Author

+

Samuel Chen, Janani Ravi

+
+ +
+

Examples

+ 
if (FALSE) { # \dontrun{
+IPG2Lineage()
+} # }
+
+
+
+
+ + +
+ + + + + + + diff --git a/reference/acc2Lineage.html b/reference/acc2Lineage.html new file mode 100644 index 00000000..c4eec71c --- /dev/null +++ b/reference/acc2Lineage.html @@ -0,0 +1,132 @@ + +acc2Lineage — acc2Lineage • MolEvolvR + Skip to contents + + +
+
+
+ +

acc2Lineage

+ Source: R/acc2lin.R, R/lineage.R +
acc2Lineage.Rd
+
+ +
+

This function combines 'efetchIPG()' and 'IPG2Lineage()' to map a set +of protein accessions to their assembly (GCA_ID), tax ID, and lineage.

+

Function to map protein accession numbers to lineage

+

This function combines 'efetchIPG()' and 'IPG2Lineage()' to map a set +of protein accessions to their assembly (GCA_ID), tax ID, and lineage.

+
+ +
+

Usage

+ 
acc2Lineage(
+  accessions,
+  assembly_path,
+  lineagelookup_path,
+  ipgout_path = NULL,
+  plan = "multicore"
+)
+
+acc2Lineage(
+  accessions,
+  assembly_path,
+  lineagelookup_path,
+  ipgout_path = NULL,
+  plan = "multicore"
+)
+
+ +
+

Arguments

+ + +
accessions
+

Character vector of protein accessions

+ + +
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

+ + +
ipgout_path
+

Path to write the results of the efetch run of the accessions +on the ipg database. If NULL, the file will not be written. Defaults to NULL

+ + +
plan
+
+ +
+
+

Value

+

Describe return, in detail

+
+
+

Author

+

Samuel Chen, Janani Ravi

+
+ +
+

Examples

+ 
if (FALSE) { # \dontrun{
+acc2Lineage()
+} # }
+
+
+
+ + +
+ + + + + + + diff --git a/reference/addlineage.html b/reference/addlineage.html new file mode 100644 index 00000000..09aa1dfd --- /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()
+} # }
+
+
+
+ + +
+ + + + + + + diff --git a/reference/count_to_sunburst.html b/reference/count_to_sunburst.html index fd609849..b4bef04d 100644 --- a/reference/count_to_sunburst.html +++ b/reference/count_to_sunburst.html @@ -90,21 +90,21 @@

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