calcSemanticSimilarity: Calculate semantic similarity

In waldronlab/BugSigDBStats: BugSigDB Stats and Analysis

Calculate semantic similarity

Description

calcSemanticSimilarity calculates the pairwise semantic similarity between two sets of signature files exported from BugSigDB.org.

Usage

calcSemanticSimilarity(file1, file2)

Arguments

file1	Signature exported from BugSigDB.org.
file2	Signature exported from BugSigDB.org.

Examples

## Not run: 

library(tidyr)
library(tibble)

## Download files froom BugSigDB's drilldown ##

file1_url <- "https://bugsigdb.org/w/index.php?title=Special:Ask&x=-5B-5BCategory%3ASignatures-5D-5D-20-5B-5BModification-20date%3A%3A%2B-5D-5D-20-5B-5BBase-20page.Location-20of-20subjects%3A%3AAustralia-5D-5D%2F-3FOriginal-20page-20name%3DSignature-20page-20name%2F-3FRelated-20experiment%3DExperiment%2F-3FRelated-20study%3DStudy%2F-3FSource-20data%3DSource%2F-3FCurated-20date%2F-3FCurator%2F-3FRevision-20editor%2F-3FDescription%2F-3FAbundance-20in-20Group-201%2F-3FNCBI-20export%3DMetaPhlAn-20taxon-20names%2F-3FNCBI-20export-20ids-20sc%3DNCBI-20Taxonomy-20IDs%2F-3FState%2F-3FReviewer&mainlabel=-&limit=5000&offset=0&format=csv&searchlabel=%3Cdiv%20class%3D%22mw-ui-button%20mw-ui-quiet%20mw-ui-progressive%20rounded-0%22%3ESignatures%3C%2Fdiv%3E&filename=signatures-filtered-australia.csv"
file1 <- tempfile()
download.file(url = file1_url, destfile = file1)

file2_url <- "https://bugsigdb.org/w/index.php?title=Special:Ask&x=-5B-5BCategory%3ASignatures-5D-5D-20-5B-5BModification-20date%3A%3A%2B-5D-5D-20-5B-5BBase-20page.Location-20of-20subjects%3A%3AUnited-20States-20of-20America-5D-5D%2F-3FOriginal-20page-20name%3DSignature-20page-20name%2F-3FRelated-20experiment%3DExperiment%2F-3FRelated-20study%3DStudy%2F-3FSource-20data%3DSource%2F-3FCurated-20date%2F-3FCurator%2F-3FRevision-20editor%2F-3FDescription%2F-3FAbundance-20in-20Group-201%2F-3FNCBI-20export%3DMetaPhlAn-20taxon-20names%2F-3FNCBI-20export-20ids-20sc%3DNCBI-20Taxonomy-20IDs%2F-3FState%2F-3FReviewer&mainlabel=-&limit=5000&offset=0&format=csv&searchlabel=%3Cdiv%20class%3D%22mw-ui-button%20mw-ui-quiet%20mw-ui-progressive%20rounded-0%22%3ESignatures%3C%2Fdiv%3E&filename=signatures-filtered-united-states-of-america.csv"
file2 <- tempfile()
download.file(url = file2_url, destfile = file2)

## Calculate semantic similarity between pairs of signatures ##

output <- calcSemanticSimilarity(file1, file2)
head(output)

## Conver output to a matrix ##

mat <- pivot_wider(
    output, names_from = sig2, values_from = semantic_similarity
    ) |> 
    tibble::column_to_rownames(var = "sig1") |> 
    as.data.frame() |> 
    as.matrix()

dim(mat)
mat[1:5, 1:5]


## End(Not run)

waldronlab/BugSigDBStats documentation built on Oct. 21, 2023, 6:11 a.m.