PlotOrgn: Plot a wordcloud of the organisms in a palm.sra object or...

In ababaian/palmid: Viral RNA Dependent RNA Polymerase Analysis Suite

Plot a wordcloud of the organisms in a palm.sra object or orgn.vec

Description

Plot a wordcloud of the organisms in a palm.sra object or orgn.vec

Usage

PlotOrgn(palm.sra = NULL, orgn.vec = NULL, freq = TRUE)

Arguments

palm.sra	data.frame, created from get.palmSra() [NULL]
orgn.vec	character, vector of "scientific_name" from sra run table [NULL]
freq	boolean, scale words by frequency, else by identity [TRUE]

Value

A ggwordcloud object of the "ntop" frequent terms

Examples

# Retrive organism identifiers from SRA Run Info Table
# palm.orgn <- get.sraOrgn(run_ids, con)

# Load Waxsystermes Exampel data
data("waxsys.palm.sra")

# Create wordcloud of organism terms
# using column "scientific_name" in data.frame

# Scaled by frequency of organism term in all of data.frame
PlotOrgn( waxsys.palm.sra )

# Scaled by proximity of organism tag to input sequence (pident)
PlotOrgn( waxsys.palm.sra , freq = FALSE)

ababaian/palmid documentation built on July 1, 2023, 1:09 a.m.