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(v0.6.1.9047) ggplot fix
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@ -20,3 +20,4 @@ vignettes/*.R
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^CRAN-RELEASE$
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packrat/lib*/
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packrat/src/
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cran-comments.md
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 0.6.1.9046
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Version: 0.6.1.9047
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Date: 2019-05-31
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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41
R/zzz.R
41
R/zzz.R
@ -29,10 +29,6 @@
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microorganisms.oldDT$fullname_lower <- tolower(microorganisms.oldDT$fullname)
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setkey(microorganisms.oldDT, col_id, fullname)
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assign(x = "microorganisms",
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value = make(),
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envir = asNamespace("AMR"))
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assign(x = "microorganismsDT",
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value = make_DT(),
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envir = asNamespace("AMR"))
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@ -55,44 +51,9 @@
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}
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#' @importFrom dplyr mutate case_when
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make <- function() {
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AMR::microorganisms %>%
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mutate(prevalence = case_when(
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class == "Gammaproteobacteria"
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| genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
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| mo == "UNKNOWN"
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~ 1,
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phylum %in% c("Proteobacteria",
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"Firmicutes",
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"Actinobacteria",
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"Sarcomastigophora")
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| genus %in% c("Aspergillus",
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"Bacteroides",
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"Candida",
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"Capnocytophaga",
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"Chryseobacterium",
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"Cryptococcus",
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"Elisabethkingia",
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"Flavobacterium",
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"Fusobacterium",
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"Giardia",
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"Leptotrichia",
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"Mycoplasma",
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"Prevotella",
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"Rhodotorula",
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"Treponema",
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"Trichophyton",
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"Ureaplasma")
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| rank %in% c("kingdom", "phylum", "class", "order", "family")
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~ 2,
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TRUE ~ 3
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))
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}
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#' @importFrom data.table as.data.table setkey
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make_DT <- function() {
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microorganismsDT <- as.data.table(make())
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microorganismsDT <- as.data.table(AMR::microorganisms)
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microorganismsDT$fullname_lower <- tolower(microorganismsDT$fullname)
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setkey(microorganismsDT,
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prevalence,
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Binary file not shown.
@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
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</span>
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</div>
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@ -42,7 +42,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
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</span>
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</div>
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@ -80,7 +80,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
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</span>
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</div>
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@ -485,7 +485,7 @@
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<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>,
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<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Top Three Microorganisms In Blood Culture Isolates"</span>,
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<span class='kw'>subtitle</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/expression'>expression</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Only First Isolates, CoNS grouped according to Becker "</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/grDevices/topics/plotmath'>italic</a></span>(<span class='st'>"et al."</span>), <span class='st'>" (2014)"</span>)),
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<span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Antibiotic (Ears-Net code)"</span>)
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<span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Antibiotic (EARS-Net code)"</span>)
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<span class='co'># }</span></pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
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</span>
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</div>
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@ -452,6 +452,39 @@ MOs <- MOs %>%
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sum(duplicated(MOs$mo))
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colnames(MOs)
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# set prevalence per species
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MOs <- MOs %>%
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mutate(prevalence = case_when(
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class == "Gammaproteobacteria"
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| genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
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| mo == "UNKNOWN"
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~ 1,
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phylum %in% c("Proteobacteria",
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"Firmicutes",
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"Actinobacteria",
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"Sarcomastigophora")
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| genus %in% c("Aspergillus",
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"Bacteroides",
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"Candida",
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"Capnocytophaga",
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"Chryseobacterium",
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"Cryptococcus",
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"Elisabethkingia",
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"Flavobacterium",
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"Fusobacterium",
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"Giardia",
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"Leptotrichia",
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"Mycoplasma",
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"Prevotella",
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"Rhodotorula",
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"Treponema",
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"Trichophyton",
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"Ureaplasma")
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| rank %in% c("kingdom", "phylum", "class", "order", "family")
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~ 2,
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TRUE ~ 3
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))
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# save it
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MOs <- as.data.frame(MOs %>% arrange(fullname), stringsAsFactors = FALSE)
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MOs.old <- as.data.frame(MOs.old, stringsAsFactors = FALSE)
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@ -59,9 +59,6 @@ test_that("ggplot_rsi works", {
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summarise_all(count_IR) %>% as.double()
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)
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expect_equal(colnames(getlbls(septic_patients %>% select(AMC, CIP))),
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c("Interpretation", "Antibiotic", "Value", "lbl"))
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expect_error(ggplot_rsi(septic_patients, fun = "invalid"))
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expect_error(geom_rsi(septic_patients, fun = "invalid"))
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