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< h1 > AMR plots with < code > ggplot2< / code > < / h1 >
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< small class = "dont-index" > Source: < a href = 'https://github.com/msberends/AMR/blob/master/R/ggplot_rsi.R' > < code > R/ggplot_rsi.R< / code > < / a > < / small >
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< div class = "hidden name" > < code > ggplot_rsi.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
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< p > Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on < a href = 'https://ggplot2.tidyverse.org/reference/ggplot.html' > ggplot2< / a > functions.< / p >
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< / div >
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< pre class = "usage" > < span class = 'fu' > ggplot_rsi< / span > (
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< span class = 'kw' > data< / span > ,
position = < span class = 'kw' > NULL< / span > ,
x = < span class = 'st' > "antibiotic"< / span > ,
fill = < span class = 'st' > "interpretation"< / span > ,
facet = < span class = 'kw' > NULL< / span > ,
breaks = < span class = 'fu' > < a href = 'https://rdrr.io/r/base/seq.html' > seq< / a > < / span > (< span class = 'fl' > 0< / span > , < span class = 'fl' > 1< / span > , < span class = 'fl' > 0.1< / span > ),
limits = < span class = 'kw' > NULL< / span > ,
translate_ab = < span class = 'st' > "name"< / span > ,
combine_SI = < span class = 'fl' > TRUE< / span > ,
combine_IR = < span class = 'fl' > FALSE< / span > ,
language = < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (),
nrow = < span class = 'kw' > NULL< / span > ,
colours = < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > (S = < span class = 'st' > "#61a8ff"< / span > , SI = < span class = 'st' > "#61a8ff"< / span > , I = < span class = 'st' > "#61f7ff"< / span > , IR = < span class = 'st' > "#ff6961"< / span > , R =
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< span class = 'st' > "#ff6961"< / span > ),
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datalabels = < span class = 'fl' > TRUE< / span > ,
datalabels.size = < span class = 'fl' > 2.5< / span > ,
datalabels.colour = < span class = 'st' > "gray15"< / span > ,
title = < span class = 'kw' > NULL< / span > ,
subtitle = < span class = 'kw' > NULL< / span > ,
caption = < span class = 'kw' > NULL< / span > ,
x.title = < span class = 'st' > "Antimicrobial"< / span > ,
y.title = < span class = 'st' > "Proportion"< / span > ,
< span class = 'kw' > ...< / span >
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)
< span class = 'fu' > geom_rsi< / span > (
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position = < span class = 'kw' > NULL< / span > ,
x = < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > (< span class = 'st' > "antibiotic"< / span > , < span class = 'st' > "interpretation"< / span > ),
fill = < span class = 'st' > "interpretation"< / span > ,
translate_ab = < span class = 'st' > "name"< / span > ,
language = < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (),
combine_SI = < span class = 'fl' > TRUE< / span > ,
combine_IR = < span class = 'fl' > FALSE< / span > ,
< span class = 'kw' > ...< / span >
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)
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< span class = 'fu' > facet_rsi< / span > (facet = < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > (< span class = 'st' > "interpretation"< / span > , < span class = 'st' > "antibiotic"< / span > ), nrow = < span class = 'kw' > NULL< / span > )
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< span class = 'fu' > scale_y_percent< / span > (breaks = < span class = 'fu' > < a href = 'https://rdrr.io/r/base/seq.html' > seq< / a > < / span > (< span class = 'fl' > 0< / span > , < span class = 'fl' > 1< / span > , < span class = 'fl' > 0.1< / span > ), limits = < span class = 'kw' > NULL< / span > )
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< span class = 'fu' > scale_rsi_colours< / span > (
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colours = < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > (S = < span class = 'st' > "#61a8ff"< / span > , SI = < span class = 'st' > "#61a8ff"< / span > , I = < span class = 'st' > "#61f7ff"< / span > , IR = < span class = 'st' > "#ff6961"< / span > , R =
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< span class = 'st' > "#ff6961"< / span > )
)
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< span class = 'fu' > theme_rsi< / span > ()
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< span class = 'fu' > labels_rsi_count< / span > (
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position = < span class = 'kw' > NULL< / span > ,
x = < span class = 'st' > "antibiotic"< / span > ,
translate_ab = < span class = 'st' > "name"< / span > ,
combine_SI = < span class = 'fl' > TRUE< / span > ,
combine_IR = < span class = 'fl' > FALSE< / span > ,
datalabels.size = < span class = 'fl' > 3< / span > ,
datalabels.colour = < span class = 'st' > "gray15"< / span >
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)< / pre >
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< h2 class = "hasAnchor" id = "arguments" > < a class = "anchor" href = "#arguments" > < / a > Arguments< / h2 >
< table class = "ref-arguments" >
< colgroup > < col class = "name" / > < col class = "desc" / > < / colgroup >
< tr >
< th > data< / th >
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< td > < p > a < code > < a href = 'https://rdrr.io/r/base/data.frame.html' > data.frame< / a > < / code > with column(s) of class < code > < a href = 'as.rsi.html' > rsi< / a > < / code > (see < code > < a href = 'as.rsi.html' > as.rsi()< / a > < / code > )< / p > < / td >
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< / tr >
< tr >
< th > position< / th >
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< td > < p > position adjustment of bars, either < code > "fill"< / code > , < code > "stack"< / code > or < code > "dodge"< / code > < / p > < / td >
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< / tr >
< tr >
< th > x< / th >
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< td > < p > variable to show on x axis, either < code > "antibiotic"< / code > (default) or < code > "interpretation"< / code > or a grouping variable< / p > < / td >
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< / tr >
< tr >
< th > fill< / th >
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< td > < p > variable to categorise using the plots legend, either < code > "antibiotic"< / code > (default) or < code > "interpretation"< / code > or a grouping variable< / p > < / td >
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< / tr >
< tr >
< th > facet< / th >
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< td > < p > variable to split plots by, either < code > "interpretation"< / code > (default) or < code > "antibiotic"< / code > or a grouping variable< / p > < / td >
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< / tr >
< tr >
< th > breaks< / th >
< td > < p > numeric vector of positions< / p > < / td >
< / tr >
< tr >
< th > limits< / th >
< td > < p > numeric vector of length two providing limits of the scale, use < code > NA< / code > to refer to the existing minimum or maximum< / p > < / td >
< / tr >
< tr >
< th > translate_ab< / th >
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< td > < p > a column name of the < a href = 'antibiotics.html' > antibiotics< / a > data set to translate the antibiotic abbreviations to, using < code > < a href = 'ab_property.html' > ab_property()< / a > < / code > . Use a value< / p > < / td >
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< / tr >
< tr >
< th > combine_SI< / th >
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< td > < p > a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter < code > combine_IR< / code > , but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is < code > TRUE< / code > .< / p > < / td >
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< / tr >
< tr >
< th > combine_IR< / th >
< td > < p > a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter < code > combine_SI< / code > .< / p > < / td >
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< / tr >
< tr >
< th > language< / th >
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< td > < p > language of the returned text, defaults to system language (see < code > < a href = 'translate.html' > get_locale()< / a > < / code > ) and can also be set with < code > < a href = 'https://rdrr.io/r/base/options.html' > getOption("AMR_locale")< / a > < / code > . Use < code > language = NULL< / code > or < code > language = ""< / code > to prevent translation.< / p > < / td >
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< / tr >
< tr >
< th > nrow< / th >
< td > < p > (when using < code > facet< / code > ) number of rows< / p > < / td >
< / tr >
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< tr >
< th > colours< / th >
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< td > < p > a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be < code > FALSE< / code > to use default [ggplot2][< code > < a href = 'https://ggplot2.tidyverse.org/reference/ggplot.html' > ggplot2::ggplot()< / a > < / code > colours.< / p > < / td >
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< / tr >
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< tr >
< th > datalabels< / th >
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< td > < p > show datalabels using < code > labels_rsi_count()< / code > < / p > < / td >
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< / tr >
< tr >
< th > datalabels.size< / th >
< td > < p > size of the datalabels< / p > < / td >
< / tr >
< tr >
< th > datalabels.colour< / th >
< td > < p > colour of the datalabels< / p > < / td >
< / tr >
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< tr >
< th > title< / th >
< td > < p > text to show as title of the plot< / p > < / td >
< / tr >
< tr >
< th > subtitle< / th >
< td > < p > text to show as subtitle of the plot< / p > < / td >
< / tr >
< tr >
< th > caption< / th >
< td > < p > text to show as caption of the plot< / p > < / td >
< / tr >
< tr >
< th > x.title< / th >
< td > < p > text to show as x axis description< / p > < / td >
< / tr >
< tr >
< th > y.title< / th >
< td > < p > text to show as y axis description< / p > < / td >
< / tr >
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< tr >
< th > ...< / th >
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< td > < p > other parameters passed on to < code > geom_rsi()< / code > < / p > < / td >
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< / tr >
< / table >
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< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
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< p > At default, the names of antibiotics will be shown on the plots using < code > < a href = 'ab_property.html' > ab_name()< / a > < / code > . This can be set with the < code > translate_ab< / code > parameter. See < code > < a href = 'count.html' > count_df()< / a > < / code > .< / p > < h3 > The functions< / h3 >
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< p > < code > geom_rsi()< / code > will take any variable from the data that has an < code > < a href = 'as.rsi.html' > rsi< / a > < / code > class (created with < code > < a href = 'as.rsi.html' > as.rsi()< / a > < / code > ) using < code > < a href = 'proportion.html' > rsi_df()< / a > < / code > and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.< / p >
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< p > < code > facet_rsi()< / code > creates 2d plots (at default based on S/I/R) using < code > < a href = 'https://ggplot2.tidyverse.org/reference/facet_wrap.html' > ggplot2::facet_wrap()< / a > < / code > .< / p >
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< p > < code > scale_y_percent()< / code > transforms the y axis to a 0 to 100% range using < code > < a href = 'https://ggplot2.tidyverse.org/reference/scale_continuous.html' > ggplot2::scale_y_continuous()< / a > < / code > .< / p >
< p > < code > scale_rsi_colours()< / code > sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using < code > < a href = 'https://ggplot2.tidyverse.org/reference/scale_manual.html' > ggplot2::scale_fill_manual()< / a > < / code > .< / p >
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< p > < code > theme_rsi()< / code > is a [ggplot2 theme][< code > < a href = 'https://ggplot2.tidyverse.org/reference/theme.html' > ggplot2::theme()< / a > < / code > with minimal distraction.< / p >
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< p > < code > labels_rsi_count()< / code > print datalabels on the bars with percentage and amount of isolates using < code > < a href = 'https://ggplot2.tidyverse.org/reference/geom_text.html' > ggplot2::geom_text()< / a > < / code > .< / p >
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< p > < code > ggplot_rsi()< / code > is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (< code > %> %< / code > ). See Examples.< / p >
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< h2 class = "hasAnchor" id = "maturing-lifecycle" > < a class = "anchor" href = "#maturing-lifecycle" > < / a > Maturing lifecycle< / h2 >
< p > < img src = 'figures/lifecycle_maturing.svg' style = margin-bottom:5px / > < br / >
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The < a href = 'lifecycle.html' > lifecycle< / a > of this function is < strong > maturing< / strong > . The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome < a href = 'https://github.com/msberends/AMR/issues' > to suggest changes at our repository< / a > or < a href = 'AMR.html' > write us an email (see section 'Contact Us')< / a > .< / p >
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< h2 class = "hasAnchor" id = "read-more-on-our-website-" > < a class = "anchor" href = "#read-more-on-our-website-" > < / a > Read more on our website!< / h2 >
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< p > On our website < a href = 'https://msberends.github.io/AMR' > https://msberends.github.io/AMR< / a > you can find < a href = 'https://msberends.github.io/AMR/articles/AMR.html' > a comprehensive tutorial< / a > about how to conduct AMR analysis, the < a href = 'https://msberends.github.io/AMR/reference' > complete documentation of all functions< / a > (which reads a lot easier than here in R) and < a href = 'https://msberends.github.io/AMR/articles/WHONET.html' > an example analysis using WHONET data< / a > . As we would like to better understand the backgrounds and needs of our users, please < a href = 'https://msberends.github.io/AMR/survey.html' > participate in our survey< / a > !< / p >
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< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
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< pre class = "examples" > < span class = 'co' > if< / span > (< span class = 'fu' > < a href = 'https://rdrr.io/r/base/library.html' > require< / a > < / span > (< span class = 'st' > < a href = 'http://ggplot2.tidyverse.org' > "ggplot2"< / a > < / span > ) < span class = 'op' > & < / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/library.html' > require< / a > < / span > (< span class = 'st' > < a href = 'https://dplyr.tidyverse.org' > "dplyr"< / a > < / span > )) {
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< span class = 'co' > # get antimicrobial results for drugs against a UTI:< / span >
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< span class = 'fu' > < a href = 'https://ggplot2.tidyverse.org/reference/ggplot.html' > ggplot< / a > < / span > (< span class = 'kw' > example_isolates< / span > < span class = 'op' > %> %< / span > < span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select< / a > < / span > (< span class = 'kw' > AMX< / span > , < span class = 'kw' > NIT< / span > , < span class = 'kw' > FOS< / span > , < span class = 'kw' > TMP< / span > , < span class = 'kw' > CIP< / span > )) < span class = 'op' > +< / span >
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< span class = 'fu' > geom_rsi< / span > ()
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< span class = 'co' > # prettify the plot using some additional functions:< / span >
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< span class = 'kw' > df< / span > < span class = 'op' > < -< / span > < span class = 'kw' > example_isolates< / span > < span class = 'op' > %> %< / span > < span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select< / a > < / span > (< span class = 'kw' > AMX< / span > , < span class = 'kw' > NIT< / span > , < span class = 'kw' > FOS< / span > , < span class = 'kw' > TMP< / span > , < span class = 'kw' > CIP< / span > )
< span class = 'fu' > < a href = 'https://ggplot2.tidyverse.org/reference/ggplot.html' > ggplot< / a > < / span > (< span class = 'kw' > df< / span > ) < span class = 'op' > +< / span >
< span class = 'fu' > geom_rsi< / span > () < span class = 'op' > +< / span >
< span class = 'fu' > scale_y_percent< / span > () < span class = 'op' > +< / span >
< span class = 'fu' > scale_rsi_colours< / span > () < span class = 'op' > +< / span >
< span class = 'fu' > labels_rsi_count< / span > () < span class = 'op' > +< / span >
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< span class = 'fu' > theme_rsi< / span > ()
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< span class = 'co' > # or better yet, simplify this using the wrapper function - a single command:< / span >
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< span class = 'kw' > example_isolates< / span > < span class = 'op' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select< / a > < / span > (< span class = 'kw' > AMX< / span > , < span class = 'kw' > NIT< / span > , < span class = 'kw' > FOS< / span > , < span class = 'kw' > TMP< / span > , < span class = 'kw' > CIP< / span > ) < span class = 'op' > %> %< / span >
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< span class = 'fu' > ggplot_rsi< / span > ()
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< span class = 'co' > # get only proportions and no counts:< / span >
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< span class = 'kw' > example_isolates< / span > < span class = 'op' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select< / a > < / span > (< span class = 'kw' > AMX< / span > , < span class = 'kw' > NIT< / span > , < span class = 'kw' > FOS< / span > , < span class = 'kw' > TMP< / span > , < span class = 'kw' > CIP< / span > ) < span class = 'op' > %> %< / span >
< span class = 'fu' > ggplot_rsi< / span > (datalabels = < span class = 'fl' > FALSE< / span > )
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< span class = 'co' > # add other ggplot2 parameters as you like:< / span >
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< span class = 'kw' > example_isolates< / span > < span class = 'op' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select< / a > < / span > (< span class = 'kw' > AMX< / span > , < span class = 'kw' > NIT< / span > , < span class = 'kw' > FOS< / span > , < span class = 'kw' > TMP< / span > , < span class = 'kw' > CIP< / span > ) < span class = 'op' > %> %< / span >
< span class = 'fu' > ggplot_rsi< / span > (width = < span class = 'fl' > 0.5< / span > ,
colour = < span class = 'st' > "black"< / span > ,
size = < span class = 'fl' > 1< / span > ,
linetype = < span class = 'fl' > 2< / span > ,
alpha = < span class = 'fl' > 0.25< / span > )
< span class = 'kw' > example_isolates< / span > < span class = 'op' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select< / a > < / span > (< span class = 'kw' > AMX< / span > ) < span class = 'op' > %> %< / span >
< span class = 'fu' > ggplot_rsi< / span > (colours = < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > (SI = < span class = 'st' > "yellow"< / span > ))
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}
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< span class = 'co' > if< / span > (< span class = 'fl' > FALSE< / span > ) {
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< span class = 'co' > # resistance of ciprofloxacine per age group< / span >
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< span class = 'kw' > example_isolates< / span > < span class = 'op' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/mutate.html' > mutate< / a > < / span > (first_isolate = < span class = 'fu' > < a href = 'first_isolate.html' > first_isolate< / a > < / span > (< span class = 'kw' > .< / span > )) < span class = 'op' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/filter.html' > filter< / a > < / span > (< span class = 'kw' > first_isolate< / span > < span class = 'op' > ==< / span > < span class = 'fl' > TRUE< / span > ,
< span class = 'kw' > mo< / span > < span class = 'op' > ==< / span > < span class = 'fu' > < a href = 'as.mo.html' > as.mo< / a > < / span > (< span class = 'st' > "E. coli"< / span > )) < span class = 'op' > %> %< / span >
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< span class = 'co' > # `age_group` is also a function of this package:< / span >
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< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/group_by.html' > group_by< / a > < / span > (age_group = < span class = 'fu' > < a href = 'age_groups.html' > age_groups< / a > < / span > (< span class = 'kw' > age< / span > )) < span class = 'op' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select< / a > < / span > (< span class = 'kw' > age_group< / span > ,
< span class = 'kw' > CIP< / span > ) < span class = 'op' > %> %< / span >
< span class = 'fu' > ggplot_rsi< / span > (x = < span class = 'st' > "age_group"< / span > )
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< span class = 'co' > # for colourblind mode, use divergent colours from the viridis package:< / span >
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< span class = 'kw' > example_isolates< / span > < span class = 'op' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select< / a > < / span > (< span class = 'kw' > AMX< / span > , < span class = 'kw' > NIT< / span > , < span class = 'kw' > FOS< / span > , < span class = 'kw' > TMP< / span > , < span class = 'kw' > CIP< / span > ) < span class = 'op' > %> %< / span >
< span class = 'fu' > ggplot_rsi< / span > () < span class = 'op' > +< / span > < span class = 'fu' > < a href = 'https://ggplot2.tidyverse.org/reference/scale_viridis.html' > scale_fill_viridis_d< / a > < / span > ()
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< span class = 'co' > # a shorter version which also adjusts data label colours:< / span >
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< span class = 'kw' > example_isolates< / span > < span class = 'op' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select< / a > < / span > (< span class = 'kw' > AMX< / span > , < span class = 'kw' > NIT< / span > , < span class = 'kw' > FOS< / span > , < span class = 'kw' > TMP< / span > , < span class = 'kw' > CIP< / span > ) < span class = 'op' > %> %< / span >
< span class = 'fu' > ggplot_rsi< / span > (colours = < span class = 'fl' > FALSE< / span > )
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< span class = 'co' > # it also supports groups (don't forget to use the group var on `x` or `facet`):< / span >
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< span class = 'kw' > example_isolates< / span > < span class = 'op' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select< / a > < / span > (< span class = 'kw' > hospital_id< / span > , < span class = 'kw' > AMX< / span > , < span class = 'kw' > NIT< / span > , < span class = 'kw' > FOS< / span > , < span class = 'kw' > TMP< / span > , < span class = 'kw' > CIP< / span > ) < span class = 'op' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/group_by.html' > group_by< / a > < / span > (< span class = 'kw' > hospital_id< / span > ) < span class = 'op' > %> %< / span >
< span class = 'fu' > ggplot_rsi< / span > (x = < span class = 'st' > "hospital_id"< / span > ,
facet = < span class = 'st' > "antibiotic"< / span > ,
nrow = < span class = 'fl' > 1< / span > ,
title = < span class = 'st' > "AMR of Anti-UTI Drugs Per Hospital"< / span > ,
x.title = < span class = 'st' > "Hospital"< / span > ,
datalabels = < span class = 'fl' > FALSE< / span > )
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}< / pre >
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< h2 data-toc-skip > Contents< / h2 >
< / nav >
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< p > Developed by < a href = 'https://www.rug.nl/staff/m.s.berends/' > Matthijs S. Berends< / a > , < a href = 'https://www.rug.nl/staff/c.f.luz/' > Christian F. Luz< / a > , < a href = 'https://www.rug.nl/staff/a.w.friedrich/' > Alexander W. Friedrich< / a > , < a href = 'https://www.rug.nl/staff/b.sinha/' > Bhanu N. M. Sinha< / a > , < a href = 'https://www.rug.nl/staff/c.j.albers/' > Casper J. Albers< / a > , < a href = 'https://www.rug.nl/staff/c.glasner/' > Corinna Glasner< / a > .< / p >
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< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.5.1.9000.< / p >
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