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ggplot2_rsi fix

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dr. M.S. (Matthijs) Berends
2018-09-13 14:48:34 +02:00
parent cb0d74a4f0
commit d049ec9e69
3 changed files with 77 additions and 34 deletions
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30
man/ggplot_rsi.Rd
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@ -28,7 +28,7 @@ theme_rsi()
\arguments{
\item{data}{a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})}
\item{position}{position adjustment of bars, either \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"} (default when \code{fun} is \code{\link{count_df}})}
\item{position}{position adjustment of bars, either \code{"fill"}, \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"} (default when \code{fun} is \code{\link{count_df}})}
\item{x}{variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable}
@ -75,7 +75,6 @@ ggplot(septic_patients \%>\% select(amox, nitr, fosf, trim, cipr)) +
df <- septic_patients[, c("amox", "nitr", "fosf", "trim", "cipr")]
ggplot(df) +
geom_rsi() +
facet_rsi() +
scale_y_percent() +
scale_rsi_colours() +
theme_rsi()
@ -106,12 +105,12 @@ septic_patients \%>\%
ggplot_rsi() + scale_fill_viridis_d()
# it also supports groups (don't forget to use the group on `x` or `facet`):
# it also supports groups (don't forget to use the group var on `x` or `facet`):
septic_patients \%>\%
select(hospital_id, amox, nitr, fosf, trim, cipr) \%>\%
group_by(hospital_id) \%>\%
ggplot_rsi(x = "hospital_id",
facet = "Antibiotic",
ggplot_rsi(x = hospital_id,
facet = Antibiotic,
nrow = 1) +
labs(title = "AMR of Anti-UTI Drugs Per Hospital",
x = "Hospital")
@ -120,8 +119,8 @@ septic_patients \%>\%
septic_patients \%>\%
# create new bacterial ID's, with all CoNS under the same group (Becker et al.)
mutate(mo = as.mo(mo, Becker = TRUE)) \%>\%
# filter on top 2 bacterial ID's
filter(mo \%in\% top_freq(freq(.$mo), 2)) \%>\%
# filter on top three bacterial ID's
filter(mo \%in\% top_freq(freq(.$mo), 3)) \%>\%
# determine first isolates
mutate(first_isolate = first_isolate(.,
col_date = "date",
@ -129,17 +128,18 @@ septic_patients \%>\%
col_mo = "mo")) \%>\%
# filter on first isolates
filter(first_isolate == TRUE) \%>\%
# join the `microorganisms` data set
left_join_microorganisms() \%>\%
# select full name and some antiseptic drugs
select(mo = fullname,
cfur, gent, cipr) \%>\%
# get short MO names (like "E. coli")
mutate(mo = mo_shortname(mo, Becker = TRUE)) \%>\%
# select this short name and some antiseptic drugs
select(mo, cfur, gent, cipr) \%>\%
# group by MO
group_by(mo) \%>\%
# plot the thing, putting MOs on the facet
ggplot_rsi(x = "Antibiotic",
facet = "mo") +
labs(title = "AMR of Top Two Microorganisms In Blood Culture Isolates",
ggplot_rsi(x = Antibiotic,
facet = mo,
translate_ab = FALSE,
nrow = 1) +
labs(title = "AMR of Top Three Microorganisms In Blood Culture Isolates",
subtitle = "Only First Isolates, CoNS grouped according to Becker et al. (2014)",
x = "Microorganisms")
}