plot_gene: Plot gene expression
In RVA: RNAseq Visualization Automation

Description Usage Arguments Details Value References Examples

This is the function to process the gene count table to show gene expression variations over time or across groups.

plot_gene(
  data = ~dat,
  anno = ~meta,
  gene.names = c("AAAS", "A2ML1", "AADACL3"),
  ct.table.id.type = "ENSEMBL",
  gene.id.type = "SYMBOL",
  treatment = "Treatment",
  sample.id = "sample_id",
  time = "day",
  log.option = TRUE,
  plot.save.to = NULL,
  input.type = "count"
)

`data`	Count table in the format of dataframe with gene id as row.names.
`anno`	Annotation table that provides design information.
`gene.names`	Genes to be visualized, in the format of character vector.
`ct.table.id.type`	The gene id format in `data` should be one of: ACCNUM, ALIAS, ENSEMBL, ENSEMBLPROT, ENSEMBLTRANS, ENTREZID, ENZYME, EVIDENCE, EVIDENCEALL, GENENAME, GO, GOALL, IPI, MAP, OMIM, ONTOLOGY, ONTOLOGYALL, PATH, PFAM, PMID, PROSITE, REFSEQ, SYMBOL, UCSCKG, UNIGENE, UNIPROT.
`gene.id.type`	The gene id format of `gene.names`, should be one of: ACCNUM, ALIAS, ENSEMBL, ENSEMBLPROT, ENSEMBLTRANS, ENTREZID, ENZYME, EVIDENCE, EVIDENCEALL, GENENAME, GO, GOALL, IPI, MAP, OMIM, ONTOLOGY, ONTOLOGYALL, PATH, PFAM, PMID, PROSITE, REFSEQ, SYMBOL, UCSCKG, UNIGENE, UNIPROT.
`treatment`	The column name to specify treatment groups.
`sample.id`	The column name to specify sample IDs.
`time`	The column name to specify different time points.
`log.option`	Logical option, whether to log2 transform the CPM as y-axis. Default = True.
`plot.save.to`	The address to save the plot from simplified cutoff combination with FDR of 0.01, 0.05, 0.1, and 0.2.
`input.type`	One of `count` or `cpm` indicating what the input data type is. If `count`, the CPM of the input data will be calculated using `edgeR::cpm()`. Default = `count`.