Identify Antimicrobial Resistance Positive Plasmids from Blast Results
Description
This function loads the imported blast results, identifies which plasmids
carry AMR genes at highest identity. May have issues with multiple genes per
plasmid, currently optimized for identifying one of two genes
Usage
amr_positives(blast.results)
amr_positives(blast.results)
Arguments
blast.results |
Blast results loaded from read_blast or from Global Env
|
Value
Two column DF of plasmid names and genes present
Examples
## Not run:
amr_positives(blastdata)
## End(Not run)
amr_positives(blastdata)
Adds the AMR_gene column to report
Description
Appends the results of amr_positives to the report
in column AMR_gene, missing have "-" instead
Usage
amr_presence(report, pos.samples)
amr_presence(report, pos.samples)
Arguments
Value
Report with AMR_genes added
See Also
subsampler, combine_results
Examples
## Not run:
amr_presence(report, pos.samples)
## End(Not run)
amr_presence(report, pos.samples)
Blast Results Parser Function
Description
Loads the imported blast results, extracts desired columns, Create new column of ratio between hit
length to query length - higher as denominator, adjusts pID by this ratio. Any AMR results are removed from the returned df.
Usage
blast_parser(blast.results)
blast_parser(blast.results)
Arguments
blast.results |
Blast results loaded from read_blast or Global Env
|
Value
Blast table with pID adjusted by ratio of hit length to query length (larger as denominator)
Examples
## Not run:
blast_parser(blastdata)
## End(Not run)
blast_parser(blastdata)
Example Table of Blast Results
Description
Example Table of Blast Results
Usage
data(blastdata)
data(blastdata)
Format
Dataframe.
Source
Strains graciously provided by the authors of the following papers:
Complete Genome and Plasmid Sequences of Three Canadian Isolates of
Salmonella enterica subsp. enterica Serovar Heidelberg from Human
and Food Sources. 2016 Labbe et al.
PMID: 26769926
Complete Sequence of Four Multidrug-Resistant MOBQ1 Plasmids Harboring
blaGES-5 Isolated from Escherichia coli and Serratia marcescens
Persisting in a Hospital in Canada. 2015 Boyd et al.
PMID: 25545311
Colistin-Nonsusceptible Pseudomonas aeruginosa Sequence Type 654 with
blaNDM-1 Arrives in North America. 2016 Mataseje et al.
PMID: 26824951
References
None Yet
(PubMed)
Examples
data(blastdata)
data(blastdata)
Combines SRST2 and Blast results into a single dataframe
Description
Combines blast and SRST2 results, cuts to desired columns (Sample,
Plasmid, Inc_group, Coverage, Divergence, Length, Clusterid), matches
plasmids to BR and appends simplified INC names, all future
modifications are done to this dataframe
Usage
combine_results(sr, br)
combine_results(sr, br)
Arguments
sr |
SRST2 results loaded from read_srst2
|
br |
Blast results parsed by blast_parser
|
Value
Seven column dataframe of SRST2 results now including INC groups
Examples
## Not run:
combine_results(example_srst2_results, example_blast_results)
## End(Not run)
combine_results(example_srst2_results, example_blast_results)
Create Heatmap Graphical Object
Description
Combines the tree, heatmap, and titles to create final heatmap image.
Usage
create_grob(report, grob.title = "Plasmid Profiles")
create_grob(report, grob.title = "Plasmid Profiles")
Arguments
report |
Dataframe of results
|
grob.title |
Title of heatmap
|
Value
Composite image
Examples
## Not run:
create_grob(report, grob.title="Plasmid Profiles")
## End(Not run)
create_grob(report, grob.title="Plasmid Profiles")
Create Plotly Object
Description
Builds the heatmap, creates final interactive plot.
Usage
create_plotly(report, user, api.key, post = NA, title = "Plasmid Profiles",
len.highlight = NA)
create_plotly(report, user, api.key, post = NA, title = "Plasmid Profiles",
len.highlight = NA)
Arguments
report |
Dataframe of results
|
user |
User ID for plotly web publishing
|
api.key |
API key for plotly web publishing
|
post |
Flag determines whether or not to post to plotly (default NA, no post)
|
title |
Title of heatmap
|
len.highlight |
If anything but NA will highlight the largest plasmid hit per incompatibility group
|
Value
plotly object
Examples
## Not run:
create_plotly(report, title="Plasmid Profiles")
## End(Not run)
create_plotly(report, title="Plasmid Profiles")
Defining Colours Based on a Column of Data
Description
This function uses RColorBrewer to produce palettes based on the factor levels of the identified column in a report.
Usage
define_colours(report, column)
define_colours(report, column)
Arguments
Value
Named vector of colours, names are factor levels of column supplied
Examples
## Not run:
define_colours(report, "AMR_gene")
## End(Not run)
define_colours(report, "AMR_gene")
Filecacher
Description
Creates filecache environment if needed for transferring variables
between functions.
Usage
file_cacher()
file_cacher()
Main: Run everything
Description
Run all the interim functions to produce outputs.
Can be run in order individually if desired.
-
read_blast Import the blast file, add column names
-
blast_parser Parse imported file
-
amr_positives Detect AMR positive plasmids
-
read_srst2 Import SRST2 file
-
combine_results Combine SRST2 and Blast
-
zetner_score Add Sureness value
-
amr_presence Add detected AMR to report
-
subsampler Apply filters to report
-
order_report Arrange report
-
save_files Save JPG and CSV
-
create_plotly Creates plot
-
save_files Save HTML plot
Usage
main(blast.file, srst2.file, coverage.filter = NA, sureness.filter = NA,
length.filter = NA, combine.inc = NA, plotly.user, plotly.api,
post.plotly = NA, anonymize = NA, main.title = "Plasmid Profiles")
main(blast.file, srst2.file, coverage.filter = NA, sureness.filter = NA,
length.filter = NA, combine.inc = NA, plotly.user, plotly.api,
post.plotly = NA, anonymize = NA, main.title = "Plasmid Profiles")
Arguments
blast.file |
Either system location of blast results (tsv) or dataframe
|
srst2.file |
Either system location of srst2 results (tsv) or dataframe
|
coverage.filter |
Filters results below percent read coverage specified (eg. 80)
|
sureness.filter |
Filters results below sureness specified (eg. 0.75)
|
length.filter |
Filters plasmid sequences shorter than length specified (eg. 10000)
|
combine.inc |
Flag to combine incompatibility sub-groups into their main type (set to 1)
|
plotly.user |
Enter your plotly info to upload to (Plotly)
|
plotly.api |
Enter your plotly info to upload to (Plotly)
|
post.plotly |
Flag to post to (Plotly)
|
anonymize |
Flag to post to anonymize plasmids and samples (set to 1)
|
main.title |
A title for the figure
|
Value
Saves output files in working directory
Examples
main(blastdata,
srst2data,
coverage.filter=NA,
sureness.filter=0.75,
length.filter=10000,
main.title="Example Results")
main(blastdata,
srst2data,
coverage.filter=NA,
sureness.filter=0.75,
length.filter=10000,
main.title="Example Results")
Minmax
Description
Takes two columns of numerical data,
normalizes it to ranges from 0 to 1 (0 to -1 for minimums),
sums them, arranges by sum, then returns the sorted dataframe
Usage
minmax(df, maxcol, mincol)
minmax(df, maxcol, mincol)
Arguments
df |
Dataframe
|
maxcol |
Column to normalize from 0 to 1
|
mincol |
Column to normalize from 0 to -1
|
Value
Dataframe sorted by sum of maxcol and mincol
Examples
## Not run:
minmax(report, "Length", "Coverage")
## End(Not run)
minmax(report, "Length", "Coverage")
Normalize
Description
Normalizes a vector of values to a range of 0-1
x - min(x)) / (max(x) - min(x)
Usage
normalize(x)
normalize(x)
Arguments
Value
Normalized vector of values
Examples
## Not run:
normalize(x)
## End(Not run)
normalize(x)
Order the Report
Description
Order the report first by sample order (tree), then by incompatibility group, then by sureness on each plasmid
Usage
order_report(report, anonymize = NA)
order_report(report, anonymize = NA)
Arguments
report |
Dataframe of results produced by subsampler or combine_results
|
anonymize |
Flag to anything other than NA to replace plasmid and sample names with generic names
|
Value
Ordered report
See Also
subsampler, combine_results
Examples
## Not run:
order_report(report)
## End(Not run)
order_report(report)
Create GGPLOT Heatmap
Description
Using a ggplot2 tile geometry this function will create a heatmap of values in the report
coloured by incompatibility group, with alpha values from the sureness score. The order of
samples is determined by order_report and plasmids by incompatibility group and sureness score.
Usage
plot_heatmap(report, len.highlight = NA)
plot_heatmap(report, len.highlight = NA)
Arguments
report |
Dataframe of results
|
len.highlight |
If anything but NA will highlight the largest plasmid hit per incompatibility group
|
Value
GGPLOT plotted heatmap
Examples
## Not run:
plot_heatmap(report)
## End(Not run)
plot_heatmap(report)
Blast file import function
Description
This function imports the 25 column blast file and adds column headers
Usage
read_blast(br.file)
read_blast(br.file)
Arguments
br.file |
System location of the blast file, no default.
|
Value
Dataframe of blast data with correct column headers.
Examples
## Not run:
read_blast("/data/blast_results.tsv")
## End(Not run)
read_blast("/data/blast_results.tsv")
SRST2 file import function
Description
This function imports the 14 column SRST2 file. Kind of superfluous
Usage
read_srst2(srst2.file)
read_srst2(srst2.file)
Arguments
srst2.file |
System location of the srst2 file, no default.
|
Value
Dataframe of srst2 data with correct column headers.
Examples
## Not run:
read_srst2("/data/srst2_results.tsv")
## End(Not run)
read_srst2("/data/srst2_results.tsv")
Example Complete Report after the following steps.
Blast data from attached blastdata table
SRST2 data from attached srst2data table
Description
read_blast Import the blast file, add column names
blast_parser Parse imported file
amr_positives Detect AMR positive plasmids
read_srst2 Import SRST2 file
combine_results Combine SRST2 and Blast
zetner_score Add Sureness value
amr_presence Add detected AMR to report
order_report Arrange report
Usage
data(report)
data(report)
Format
Dataframe.
Source
Strains graciously provided by the authors of the following papers:
Complete Genome and Plasmid Sequences of Three Canadian Isolates of
Salmonella enterica subsp. enterica Serovar Heidelberg from Human
and Food Sources. 2016 Labbe et al.
PMID: 26769926
Complete Sequence of Four Multidrug-Resistant MOBQ1 Plasmids Harboring
blaGES-5 Isolated from Escherichia coli and Serratia marcescens
Persisting in a Hospital in Canada. 2015 Boyd et al.
PMID: 25545311
Colistin-Nonsusceptible Pseudomonas aeruginosa Sequence Type 654 with
blaNDM-1 Arrives in North America. 2016 Mataseje et al.
PMID: 26824951
References
None Yet
(PubMed)
Examples
data(report)
data(report)
Save Files
Description
Save various files: JPG, CSV, HTML depending on parameters
Usage
save_files(report, plot.png = NA, report.csv = NA, webpage = NA,
title = "Plasmid Profiles")
save_files(report, plot.png = NA, report.csv = NA, webpage = NA,
title = "Plasmid Profiles")
Arguments
report |
Dataframe of results
|
plot.png |
Do you want to save a png? (Anything but NA)
|
report.csv |
Do you want to save a text report? (Anything but NA)
|
webpage |
Do you want to save an interactive heatmap as html? (Anything but NA)
|
title |
Enter a title for the plot
|
Value
Named vector of colours, names are factor levels of column supplied
Examples
## Not run:
save_files(report, plot.png=1, report.csv=1, webpage=NA)
## End(Not run)
save_files(report, plot.png=1, report.csv=1, webpage=NA)
Example Table of SRST2 Results
Description
Example Table of SRST2 Results
Usage
data(srst2data)
data(srst2data)
Format
Dataframe.
Source
Strains graciously provided by the authors of the following papers:
Complete Genome and Plasmid Sequences of Three Canadian Isolates of
Salmonella enterica subsp. enterica Serovar Heidelberg from Human
and Food Sources. 2016 Labbe et al.
PMID: 26769926
Complete Sequence of Four Multidrug-Resistant MOBQ1 Plasmids Harboring
blaGES-5 Isolated from Escherichia coli and Serratia marcescens
Persisting in a Hospital in Canada. 2015 Boyd et al.
PMID: 25545311
Colistin-Nonsusceptible Pseudomonas aeruginosa Sequence Type 654 with
blaNDM-1 Arrives in North America. 2016 Mataseje et al.
PMID: 26824951
References
None Yet
(PubMed)
Examples
data(srst2data)
data(srst2data)
Subsetting Results
Description
Several filters can be applied:
Coverage: Filters results below percent read coverage specified
eg. 95.9 cuts results where reads covered less than 95.9% of the total length
Sureness: Filters results below sureness specified
eg. 0.9 cuts results where the sureness falls below 0.9
Length: Filters plasmid sequences shorter than length specified
eg. 10000 cuts out results where the plasmid was less than 10kb
Incompatibility groups can also be combined (eg. Fii(S) and Fii(K) are combined into Fii)
Usage
subsampler(report, cov.filter = NA, sure.filter = NA, len.filter = NA,
inc.combine = NA)
subsampler(report, cov.filter = NA, sure.filter = NA, len.filter = NA,
inc.combine = NA)
Arguments
report |
Dataframe of results produced
by subsampler or combine_results
|
cov.filter |
Filters results below percent read coverage specified (eg. 80)
|
sure.filter |
Filters results below sureness specified (eg. 0.75)
|
len.filter |
Filters plasmid sequences shorter than length specified (eg. 10000)
|
inc.combine |
Flag to ombine incompatibility sub-groups into their main type (set to 1)
|
Value
Report with filters applied
See Also
subsampler, combine_results
Examples
## Not run:
subsampler(report, sureness.filter = 0.75, len.filter = 10000)
## End(Not run)
subsampler(report, sureness.filter = 0.75, len.filter = 10000)
Create Dendrogram Based on Plasmid Content
Description
Reads report, converts to matrix of Sample ~ Plasmid with Sureness as cell values.
Performs a hierarchical cluster analysis on a set of dissimilarities derived from the matrix.
Creates a dendrogram from this data. Returns either the HC data or the dendrogram plot
Usage
tree_maker(report, hc.only = NA)
tree_maker(report, hc.only = NA)
Arguments
report |
Dataframe of results produced
by subsampler or combine_results
|
hc.only |
Flag to return only hierarchical clustering
results instead of dendrogram plot (set to 1)
|
Value
Dendrogram object or hierarchical clustering results
See Also
subsampler, combine_results
Examples
## Not run:
tree_maker(report)
## End(Not run)
tree_maker(report)
Adds the Zetner Score column to report
Description
Runs mimmax function on Coverage and Divergence, returns sum of normalized Coverage with negative normalized Divergence
a value which is then normalized from 0 to 1.
Usage
zetner_score(report)
zetner_score(report)
Arguments
Value
Report with zetner score added
See Also
subsampler, combine_results
Examples
## Not run:
zetner_score(report)
## End(Not run)
zetner_score(report)