Skip to contents

MolEvolvR Summary

Source: R/summarize.R
MolEvolvR_summary.Rd

A collection of summary functions for the MolEvolvR package.

Function to summarize and retrieve counts by Domains & Domains+Lineage

Function to retrieve counts of how many lineages a DomArch appears in

Creates a data frame with a totalcount column

This function is designed to sum the counts column by either Genomic Context or Domain Architecture and creates a totalcount column from those sums.

Usage

summarizeByLineage(prot = "prot", column = "DomArch", by = "Lineage", query)

summarizeDomArch_ByLineage(x)

summarizeDomArch(x)

summarizeGenContext_ByDomArchLineage(x)

summarizeGenContext_ByLineage(x)

summarizeGenContext(x)

totalGenContextOrDomArchCounts(
  prot,
  column = "DomArch",
  lineage_col = "Lineage",
  cutoff = 90,
  RowsCutoff = FALSE,
  digits = 2
)

Arguments

prot

A data frame that must contain columns:

  • count

column

Character. The column to summarize, default is "DomArch".

by

A string representing the grouping column (e.g., Lineage). Default is "Lineage".

query

A string specifying the query pattern for filtering the target column. Use "all" to skip filtering and include all rows.

x

A dataframe or tibble containing the data. It must have columns named GenContext, DomArch, Lineage, and count.

lineage_col

Character. The name of the lineage column, default is "Lineage".

cutoff

Numeric. Cutoff for total count. Counts below this cutoff value will not be shown. Default is 0.

RowsCutoff

Logical. If TRUE, filters based on cumulative percentage cutoff. Default is FALSE.

digits

Numeric. Number of decimal places for percentage columns. Default is 2.

Value

A tibble summarizing the counts of occurrences of elements in the column, grouped by the by column. The result includes the number of occurrences (count) and is arranged in descending order of count.

A tibble summarizing the counts of unique domain architectures (DomArch) per lineage (Lineage). The resulting table contains three columns: DomArch, Lineage, and count, which indicates the frequency of each domain architecture for each lineage. The results are arranged in descending order of count.

A tibble summarizing each unique DomArch, along with the following columns:

  • totalcount: The total occurrences of each DomArch across all lineages.

  • totallin: The total number of unique lineages in which each DomArch appears. The results are arranged in descending order of totallin and totalcount.

A tibble summarizing each unique combination of GenContext, DomArch, and Lineage, along with the following columns:

  • GenContext: The genomic context for each entry.

  • DomArch: The domain architecture for each entry.

  • Lineage: The lineage associated with each entry.

  • count: The total number of occurrences for each combination of GenContext, DomArch, and Lineage.

The results are arranged in descending order of count.

A tibble summarizing each unique combination of GenContext and Lineage, along with the count of occurrences. The results are arranged in descending order of count.

A tibble summarizing each unique GenContext, along with the following columns:

  • totalcount: The total count for each GenContext.

  • totalDA: The number of distinct DomArch for each GenContext.

  • totallin: The number of distinct Lineage for each GenContext.

The results are arranged in descending order of totalcount, totalDA, and totallin.

A data frame with the following columns:

  • {{ column }}: Unique values from the specified column.

  • totalcount: The total count of occurrences for each unique value in the specified column.

  • IndividualCountPercent: The percentage of each totalcount relative to the overall count.

  • CumulativePercent: The cumulative percentage of total counts.

Note

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

Examples

if (FALSE) { # \dontrun{
library(tidyverse)
tibble(DomArch = c("a+b", "a+b", "b+c", "a+b"), Lineage = c("l1", "l1", "l1", "l2")) |>
    summarizeByLineage(query = "all")
} # }

if (FALSE) { # \dontrun{
summarizeDomArch_ByLineage(data1)
} # }
if (FALSE) { # \dontrun{
summarizeDomArch(data1)
} # }
if (FALSE) { # \dontrun{
summarizeGenContext_ByDomArchLineage(your_data)
} # }
if (FALSE) { # \dontrun{
summarizeGenContext_ByLineage(your_data)
} # }
if (FALSE) { # \dontrun{
summarizeGenContext(data1)
} # }
if (FALSE) { # \dontrun{
totalGenContextOrDomArchCounts(pspa - gc_lin_counts, 0, "GC")
} # }