1 About

This package aims to visualize the word and text information contained in the gene or the other omics identifiers such as microbiome, and identify important words among the clusters, and compare the clusters based on those information. It contributes to understanding the gene clusters and aid in easy interpretation and visualization. The documentation using bookdown is available here, and the web server using shinyapps.io is here.

The example visualization below shows the annotation of gene cluster network.

library(biotextgraph)
knitr::include_url("https://noriakis.github.io/cyjs_test/wordcloud")

Another example below shows summarization of 636 genes identified in differential expression analysis by BioFabric layout.

load(system.file("extdata", "sysdata.rda", package = "biotextgraph"))
net <- refseq(d3degUpAssetta2016, numWords=40, autoThresh=FALSE, tag="cor", genePlot=TRUE)
#> Input genes: 636
#>   Converted input genes: 552
#> Filter based on GeneSummary
#> Filtered 77 words (frequency and/or tfidf)
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plot_biofabric(net, color_map="tag")