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styled, unit test fix

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dr. M.S. (Matthijs) Berends
2022-08-28 10:31:50 +02:00
parent 4cb1db4554
commit 4d050aef7c
147 changed files with 10897 additions and 8169 deletions
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26
man/ggplot_pca.Rd
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@@ -114,24 +114,26 @@ The colours for labels and points can be changed by adding another scale layer f
\donttest{
if (require("dplyr")) {
# calculate the resistance per group first
resistance_data <- example_isolates \%>\%
group_by(order = mo_order(mo), # group on anything, like order
genus = mo_genus(mo)) \%>\% # and genus as we do here;
filter(n() >= 30) \%>\% # filter on only 30 results per group
summarise_if(is.rsi, resistance) # then get resistance of all drugs
# calculate the resistance per group first
resistance_data <- example_isolates \%>\%
group_by(
order = mo_order(mo), # group on anything, like order
genus = mo_genus(mo)
) \%>\% # and genus as we do here;
filter(n() >= 30) \%>\% # filter on only 30 results per group
summarise_if(is.rsi, resistance) # then get resistance of all drugs
# now conduct PCA for certain antimicrobial agents
pca_result <- resistance_data \%>\%
pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT)
pca_result <- resistance_data \%>\%
pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT)
summary(pca_result)
# old base R plotting method:
biplot(pca_result)
# new ggplot2 plotting method using this package:
ggplot_pca(pca_result)
if (require("ggplot2")) {
ggplot_pca(pca_result) +
scale_colour_viridis_d() +