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Plasmidprofiler (version 0.1.6)

Visualization of Plasmid Profile Results

Description

Contains functions developed to combine the results of querying a plasmid database using short-read sequence typing with the results of a blast analysis against the query results.

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Version

Install

install.packages('Plasmidprofiler')

Monthly Downloads

183

Version

0.1.6

License

Apache License 2.0

Maintainer

Adrian Zetner

Last Published

January 6th, 2017

Functions in Plasmidprofiler (0.1.6)

blast_parser

Blast Results Parser Function
blastdata

Example Table of Blast Results
create_grob

Create Heatmap Graphical Object
amr_presence

Adds the AMR_gene column to report
combine_results

Combines SRST2 and Blast results into a single dataframe
file_cacher

Filecacher
create_plotly

Create Plotly Object
main

Main: Run everything
define_colours

Defining Colours Based on a Column of Data
report

Example Complete Report after the following steps. Blast data from attached blastdata table SRST2 data from attached srst2data table
save_files

Save Files
minmax

Minmax
normalize

Normalize
read_blast

Blast file import function
srst2data

Example Table of SRST2 Results
order_report

Order the Report
subsampler

Subsetting Results
plot_heatmap

Create GGPLOT Heatmap
amr_positives

Identify Antimicrobial Resistance Positive Plasmids from Blast Results
tree_maker

Create Dendrogram Based on Plasmid Content
zetner_score

Adds the Zetner Score column to report
read_srst2

SRST2 file import function