From da3ce4917ad38914e08b2873edb441d9176c8e7e Mon Sep 17 00:00:00 2001 From: the-mayer <32186106+the-mayer@users.noreply.github.com> Date: Fri, 11 Oct 2024 19:52:05 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20JRaviLab?= =?UTF-8?q?/MolEvolvR@cffeb7ac1bfa1a30382f7c8528549b8414165308=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/countByColumn.html | 105 ++++++++++++++++++++++++ reference/filterByDomains.html | 117 +++++++++++++++++++++++++++ reference/filterByFrequency.html | 91 +++++++++++++++++++++ reference/findParalogs.html | 88 ++++++++++++++++++++ reference/getTopAccByLinDomArch.html | 78 ++++++++++++++++++ reference/index.html | 50 ++++++------ reference/plotIPR2Viz.html | 82 +++++++++++++++++++ reference/plotIPR2VizWeb.html | 82 +++++++++++++++++++ reference/plotSunburst.html | 8 +- reference/themeGenes2.html | 63 +++++++++++++++ reference/words2WordCounts.html | 95 ++++++++++++++++++++++ search.json | 2 +- sitemap.xml | 18 ++--- 14 files changed, 841 insertions(+), 40 deletions(-) create mode 100644 reference/countByColumn.html create mode 100644 reference/filterByDomains.html create mode 100644 reference/filterByFrequency.html create mode 100644 reference/findParalogs.html create mode 100644 reference/getTopAccByLinDomArch.html create mode 100644 reference/plotIPR2Viz.html create mode 100644 reference/plotIPR2VizWeb.html create mode 100644 reference/themeGenes2.html create mode 100644 reference/words2WordCounts.html diff --git a/pkgdown.yml b/pkgdown.yml index b96f53df..db0722a8 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 3.1.11 pkgdown: 2.1.1 pkgdown_sha: ~ articles: {} -last_built: 2024-10-11T15:08Z +last_built: 2024-10-11T19:51Z urls: reference: https://jravilab.github.io/MolEvolvR/reference article: https://jravilab.github.io/MolEvolvR/articles diff --git a/reference/countByColumn.html b/reference/countByColumn.html new file mode 100644 index 00000000..76133d05 --- /dev/null +++ b/reference/countByColumn.html @@ -0,0 +1,105 @@ + +countByColumn — countByColumn • MolEvolvR + Skip to contents + + +
+
+
+ +

countByColumn

+ Source: R/summarize.R +
countByColumn.Rd
+
+ +
+

Function to obtain element counts (DA, GC)

+
+ +
+

Usage

+ 
countByColumn(prot = prot, column = "DomArch", min.freq = 1)
+
+ +
+

Arguments

+ + +
prot
+

A data frame containing the dataset to analyze, typically with +multiple columns including the one specified by the column parameter.

+ + +
column
+

A character string specifying the name of the column to analyze. +The default is "DomArch".

+ + +
min.freq
+

An integer specifying the minimum frequency an element must +have to be included in the output. Default is 1.

+ +
+
+

Value

+

A tibble with two columns:

column
+

The unique elements from the specified column +(e.g., "DomArch").

+ +
freq
+

The frequency of each element, i.e., the number of times +each element appears in the specified column.

+ + +

The tibble is filtered to only include elements that have a frequency +greater than or equal to min.freq and does not include elements with NA +values or those starting with a hyphen ("-").

+
+ +
+

Examples

+ 
if (FALSE) { # \dontrun{
+countByColumn(prot = my_data, column = "DomArch", min.freq = 10)
+} # }
+
+
+
+ + +
+ + + + + + + diff --git a/reference/filterByDomains.html b/reference/filterByDomains.html new file mode 100644 index 00000000..dec04d70 --- /dev/null +++ b/reference/filterByDomains.html @@ -0,0 +1,117 @@ + +filterByDomains — filterByDomains • MolEvolvR + Skip to contents + + +
+
+
+ +

filterByDomains

+ Source: R/summarize.R +
filterByDomains.Rd
+
+ +
+

filterByDomains filters a data frame by identifying exact domain matches +and either keeping or removing rows with the identified domain

+
+ +
+

Usage

+ 
filterByDomains(
+  prot,
+  column = "DomArch",
+  doms_keep = c(),
+  doms_remove = c(),
+  ignore.case = FALSE
+)
+
+ +
+

Arguments

+ + +
prot
+

Dataframe to filter

+ + +
column
+

Column to search for domains in (DomArch column)

+ + +
doms_keep
+

Vector of domains that must be identified within column in order for +observation to be kept

+ + +
doms_remove
+

Vector of domains that, if found within an observation, will be removed

+ + +
ignore.case
+

Should the matching be non case sensitive

+ +
+
+

Value

+

Filtered data frame

+
+
+

Note

+

There is no need to make the domains 'regex safe', that will be handled by this function

+
+
+

Author

+

Samuel Chen, Janani Ravi

+
+ +
+

Examples

+ 
if (FALSE) { # \dontrun{
+filterByDomains()
+} # }
+
+
+
+ + +
+ + + + + + + diff --git a/reference/filterByFrequency.html b/reference/filterByFrequency.html new file mode 100644 index 00000000..97aa1fe8 --- /dev/null +++ b/reference/filterByFrequency.html @@ -0,0 +1,91 @@ + +filterByFrequency — filterByFrequency • MolEvolvR + Skip to contents + + +
+
+
+ +

filterByFrequency

+ Source: R/summarize.R +
filterByFrequency.Rd
+
+ +
+

Function to filter based on frequencies

+
+ +
+

Usage

+ 
filterByFrequency(x, min.freq)
+
+ +
+

Arguments

+ + +
x
+

A tibble (tbl_df) containing at least two columns: one for +elements (e.g., words) and one for their frequency (e.g., freq).

+ + +
min.freq
+

A numeric value specifying the minimum frequency threshold. +Only elements with frequencies greater than or equal to this value will be +retained.

+ +
+
+

Value

+

A tibble with the same structure as x, but filtered to include +only rows where the frequency is greater than or equal to min.freq.

+
+ +
+

Examples

+ 
if (FALSE) { # \dontrun{
+filterByFrequency()
+} # }
+
+
+
+ + +
+ + + + + + + diff --git a/reference/findParalogs.html b/reference/findParalogs.html new file mode 100644 index 00000000..29652a02 --- /dev/null +++ b/reference/findParalogs.html @@ -0,0 +1,88 @@ + +findParalogs — findParalogs • MolEvolvR + Skip to contents + + +
+
+
+ +

findParalogs

+ Source: R/summarize.R +
findParalogs.Rd
+
+ +
+

Creates a data frame of paralogs.

+
+ +
+

Usage

+ 
findParalogs(prot)
+
+ +
+

Arguments

+ + +
prot
+

A data frame filtered by a Query, containing columns Species and Lineage

+ +
+
+

Value

+

returns a dataframe containing paralogs and the counts.

+
+
+

Note

+

Please refer to the source code if you have alternate file formats and/or +column names.

+
+ +
+

Examples

+ 
if (FALSE) { # \dontrun{
+findParalogs(pspa)
+} # }
+
+
+
+ + +
+ + + + + + + diff --git a/reference/getTopAccByLinDomArch.html b/reference/getTopAccByLinDomArch.html new file mode 100644 index 00000000..88547eb1 --- /dev/null +++ b/reference/getTopAccByLinDomArch.html @@ -0,0 +1,78 @@ + +getTopAccByLinDomArch — getTopAccByLinDomArch • MolEvolvR + Skip to contents + + +
+
+
+ +

getTopAccByLinDomArch

+ Source: R/ipr2viz.R +
getTopAccByLinDomArch.Rd
+
+ +
+

Group by lineage + DA then take top 20

+
+ +
+

Usage

+ 
getTopAccByLinDomArch(
+  infile_full,
+  DA_col = "DomArch.Pfam",
+  lin_col = "Lineage_short",
+  n = 20,
+  query
+)
+
+ +
+

Arguments

+ + +
query
+
+ +
+ +
+ + +
+ + + + + + + diff --git a/reference/index.html b/reference/index.html index 3ca3a7f9..ef5e6f51 100644 --- a/reference/index.html +++ b/reference/index.html @@ -259,7 +259,7 @@

All functionscountByColumn() + countByColumn()
countByColumn
@@ -343,25 +343,19 @@

All functionsfilterByDomains() + filterByDomains()
filterByDomains
- filterByFrequency() + filterByFrequency()
filterByFrequency
- find_top_acc() - -
-
Group by lineage + DA then take top 20
-
- - findParalogs() + findParalogs()
findParalogs
@@ -415,6 +409,12 @@

All functionsgetTopAccByLinDomArch() + + +
getTopAccByLinDomArch
+

+ get_accnums_from_fasta_file()
@@ -433,18 +433,6 @@

All functionsipr2viz() - - -
IPR2Viz
-

- - ipr2viz_web() - -
-
IPR2Viz Web
-
- make_opts2procs()
@@ -475,6 +463,18 @@

All functionsplotIPR2Viz() + + +
plotIPR2Viz
+

+ + plotIPR2VizWeb() + +
+
plotIPR2VizWeb
+
+ plotLineageDA()
@@ -655,10 +655,10 @@

All functionstheme_genes2() + themeGenes2() -
Theme Genes2
+
themeGenes2

to_titlecase() @@ -679,7 +679,7 @@

All functionswords2WordCounts() + words2WordCounts()

words2WordCounts
diff --git a/reference/plotIPR2Viz.html b/reference/plotIPR2Viz.html new file mode 100644 index 00000000..a7c9cb79 --- /dev/null +++ b/reference/plotIPR2Viz.html @@ -0,0 +1,82 @@ + +plotIPR2Viz — plotIPR2Viz • MolEvolvR + Skip to contents + + +
+
+
+ +

plotIPR2Viz

+ Source: R/ipr2viz.R +
plotIPR2Viz.Rd
+
+ +
+

plotIPR2Viz

+
+ +
+

Usage

+ 
plotIPR2Viz(
+  infile_ipr = NULL,
+  infile_full = NULL,
+  accessions = c(),
+  analysis = c("Pfam", "Phobius", "TMHMM", "Gene3D"),
+  group_by = "Analysis",
+  topn = 20,
+  name = "Name",
+  text_size = 15,
+  query = "All"
+)
+
+ +
+

Arguments

+ + +
query
+
+ +
+ +
+ + +
+

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

+
+ +
+

Site built with pkgdown 2.1.1.

+
+ +
+ + + + + + + diff --git a/reference/plotIPR2VizWeb.html b/reference/plotIPR2VizWeb.html new file mode 100644 index 00000000..3516381b --- /dev/null +++ b/reference/plotIPR2VizWeb.html @@ -0,0 +1,82 @@ + +plotIPR2VizWeb — plotIPR2VizWeb • MolEvolvR + Skip to contents + + +
+
+
+ +

plotIPR2VizWeb

+ Source: R/ipr2viz.R +
plotIPR2VizWeb.Rd
+
+ +
+

plotIPR2VizWeb

+
+ +
+

Usage

+ 
plotIPR2VizWeb(
+  infile_ipr,
+  accessions,
+  analysis = c("Pfam", "Phobius", "TMHMM", "Gene3D"),
+  group_by = "Analysis",
+  name = "Name",
+  text_size = 15,
+  legend_name = "ShortName",
+  cols = 5,
+  rows = 10
+)
+
+ +
+

Arguments

+ + +
rows
+
+ +
+ +
+ + +
+

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

+
+ +
+

Site built with pkgdown 2.1.1.

+
+ +
+ + + + + + + diff --git a/reference/plotSunburst.html b/reference/plotSunburst.html index 4a0bda61..b4dd9a0c 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)
- +