2020-03-08 09:12:11 +01:00
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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2020-07-08 14:48:06 +02:00
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# https://github.com/msberends/AMR #
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2020-03-08 09:12:11 +01:00
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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2020-07-08 14:48:06 +02:00
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# Visit our website for more info: https://msberends.github.io/AMR. #
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2020-03-08 09:12:11 +01:00
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# ==================================================================== #
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context("pca.R")
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test_that("PCA works", {
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2020-07-30 15:15:52 +02:00
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skip_on_cran()
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2020-05-16 13:05:47 +02:00
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resistance_data <- structure(list(order = c("Bacillales", "Enterobacterales", "Enterobacterales"),
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genus = c("Staphylococcus", "Escherichia", "Klebsiella"),
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AMC = c(0.00425, 0.13062, 0.10344),
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CXM = c(0.00425, 0.05376, 0.10344),
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CTX = c(0.00000, 0.02396, 0.05172),
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TOB = c(0.02325, 0.02597, 0.10344),
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TMP = c(0.08387, 0.39141, 0.18367)),
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class = c("grouped_df", "tbl_df", "tbl", "data.frame"),
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row.names = c(NA, -3L),
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groups = structure(list(order = c("Bacillales", "Enterobacterales"),
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.rows = list(1L, 2:3)),
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row.names = c(NA, -2L),
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class = c("tbl_df", "tbl", "data.frame"),
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.drop = TRUE))
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2020-03-08 09:12:11 +01:00
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2020-03-08 11:18:59 +01:00
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pca_model <- pca(resistance_data)
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2020-03-08 09:12:11 +01:00
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2020-03-08 11:18:59 +01:00
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expect_s3_class(pca_model, "pca")
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ggplot_pca(pca_model, ellipse = TRUE)
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2020-07-28 18:39:57 +02:00
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ggplot_pca(pca_model, arrows_textangled = FALSE)
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2020-03-08 09:12:11 +01:00
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})
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