}}
diff --git a/man/SampleLocation.Rd b/man/SampleLocation.Rd
index 4cd4ae44..53d78363 100644
--- a/man/SampleLocation.Rd
+++ b/man/SampleLocation.Rd
@@ -15,6 +15,7 @@ sample_location$location_name
sample_location <- SampleLocation$parse_sample_location("65(1,F5)")
sample_location$location_name
+
}
\section{Public fields}{
\if{html}{\out{
}}
diff --git a/man/plot_standard_curve_antibody.Rd b/man/plot_standard_curve_antibody.Rd
index f6f0f727..812185ec 100644
--- a/man/plot_standard_curve_antibody.Rd
+++ b/man/plot_standard_curve_antibody.Rd
@@ -10,7 +10,7 @@ plot_standard_curve_antibody(
data_type = "Median",
file_path = NULL,
decreasing_dilution_order = TRUE,
- log_scale = c("dilutions"),
+ log_scale = c("all"),
verbose = TRUE
)
}
diff --git a/man/read_data.Rd b/man/read_data.Rd
index 58b748d8..da7ebd65 100644
--- a/man/read_data.Rd
+++ b/man/read_data.Rd
@@ -8,9 +8,9 @@ read_data(
file_path,
layout_file_path = NULL,
check_plate = TRUE,
- ...,
verbose = TRUE,
- colorize = !isTRUE(getOption("knitr.in.progress"))
+ colorize = !isTRUE(getOption("knitr.in.progress")),
+ ...
)
}
\arguments{
@@ -23,12 +23,15 @@ read_data(
\item{verbose}{if TRUE, print out the progress of the function}
\item{colorize}{if TRUE, colorize the output}
+
+\item{...}{additional arguments passed down}
}
\description{
file structure based on the https://genome.med.harvard.edu/documents/luminex/IS2.3_SW_110_eng_us.pdf page 97
and Kenya screening csv files
}
\examples{
-plate <- read_data("path/to/file.csv")
+plate_file <- system.file("extdata", "random.csv", package = "PvSTATEM")
+plate <- read_data(plate_file)
}
diff --git a/tests/testthat/test-initial-preprocessing.R b/tests/testthat/test-initial-preprocessing.R
index c6195f52..1d7b0f2d 100644
--- a/tests/testthat/test-initial-preprocessing.R
+++ b/tests/testthat/test-initial-preprocessing.R
@@ -1,35 +1,45 @@
-test_that("blank adjustment works", {
- kenya_filepath <- system.file("extdata", "kenya.csv", package = "PvSTATEM", mustWork = TRUE)
+library(testthat)
- plate <- read_data(kenya_filepath, verbose=FALSE)
+test_that("blank adjustment", {
+ plate_file <- system.file("extdata", "random.csv", package = "PvSTATEM", mustWork = TRUE)
- initial_mfi_value = plate$samples[[1]]$data["Net MFI", "Etramp5_ag1"]
- expect_equal(initial_mfi_value, 5595.5)
+ plate <- read_data(plate_file, verbose = FALSE)
+
+ initial_mfi_value <- plate$samples[[2]]$data["Median", "Etramp5_ag1"]
+ expect_equal(initial_mfi_value, 1292)
plate$blank_adjustment(inplace = T, method = "avg")
- recalculated_mfi_value = plate$samples[[1]]$data["Net MFI", "Etramp5_ag1"]
- expect_equal(recalculated_mfi_value, 5545.3333)
+ recalculated_mfi_value <- plate$samples[[2]]$data["Median", "Etramp5_ag1"]
+ expect_equal(recalculated_mfi_value, 1272)
})
test_that("plotting standard curves work", {
+ plate_file1 <- system.file("extdata", "random.csv", package = "PvSTATEM", mustWork = TRUE)
+ plate_file2 <- system.file("extdata", "random.csv", package = "PvSTATEM", mustWork = TRUE)
- kenya_filepath1 <- system.file("extdata", "kenya.csv", package = "PvSTATEM", mustWork = TRUE)
- kenya_filepath6 <- system.file("extdata", "kenya_P6.csv", package = "PvSTATEM", mustWork = TRUE)
- kenya_filepath4 <- system.file("extdata", "kenya_P4.csv", package = "PvSTATEM", mustWork = TRUE)
-
- plate1 <- read_data(kenya_filepath1, verbose=FALSE)
- plate6 <- read_data(kenya_filepath6, verbose=FALSE)
- plate4 <- read_data(kenya_filepath4, verbose=FALSE)
+ plate1 <- read_data(plate_file1, verbose = FALSE)
+ plate2 <- read_data(plate_file2, verbose = FALSE)
plate1$blank_adjustment()
- plate4$blank_adjustment()
- plate6$blank_adjustment()
+ plate2$blank_adjustment()
+
+ plates <- list(plate1, plate2)
+
+ expect_error(plot_standard_curve_antibody(plates, antibody_name = "Etramp5_ag1"), NA)
+})
+test_that("plotting standard curves fail - different dilutions", {
+ plate_file1 <- system.file("extdata", "random.csv", package = "PvSTATEM", mustWork = TRUE)
+ plate_file2 <- system.file("extdata", "random2.csv", package = "PvSTATEM", mustWork = TRUE)
+ plate1 <- read_data(plate_file1, verbose = FALSE)
+ plate2 <- read_data(plate_file2, verbose = FALSE)
- plates <- list(plate1, plate4, plate6)
+ plate1$blank_adjustment()
+ plate2$blank_adjustment()
+ plates <- list(plate1, plate2)
- expect_error(plot_standard_curve_antibody(plates, antibody_name = "Etramp5_ag1"), NA)
+ expect_error(plot_standard_curve_antibody(plates, antibody_name = "Etramp5_ag1"))
})
diff --git a/tests/testthat/test-read-data.R b/tests/testthat/test-read-data.R
index 6e57e6a8..baa2cc21 100644
--- a/tests/testthat/test-read-data.R
+++ b/tests/testthat/test-read-data.R
@@ -1,23 +1,20 @@
-test_that("reading file works", {
- kenya_filepath <- system.file("extdata", "kenya.csv", package = "PvSTATEM", mustWork = TRUE)
+test_that("reading file", {
+ plate_filepath <- system.file("extdata", "random.csv", package = "PvSTATEM", mustWork = TRUE)
- plate <- read_data(kenya_filepath, verbose=FALSE)
- expect_equal(length(plate$samples), 96)
+ plate <- read_data(plate_filepath, verbose = FALSE)
+ expect_equal(length(plate$samples), 8)
})
-test_that("reading file works", {
- oise_filepath <- system.file("extdata", "OISE.csv", package = "PvSTATEM", mustWork = TRUE)
- oise_layout_filepath <- system.file("extdata", "OISE_layout.xlsx", package = "PvSTATEM", mustWork = TRUE)
-
- plate <- read_data(oise_filepath, layout_file_path = oise_layout_filepath, check_plate = FALSE, verbose=FALSE)
- expect_equal(length(plate$samples), 96)
+test_that("reading file with layout", {
+ plate_filepath <- system.file("extdata", "random.csv", package = "PvSTATEM", mustWork = TRUE)
+ layout_filepath <- system.file("extdata", "random_layout.xlsx", package = "PvSTATEM", mustWork = TRUE)
+ plate <- read_data(plate_filepath, layout_file_path = layout_filepath, check_plate = FALSE, verbose = FALSE)
+ expect_equal(length(plate$samples), 8)
})
test_that("incorrect format detection", { # add better handling of this error
- kenya_filepath <- system.file("extdata", "kenya_P3_shifted.csv", package = "PvSTATEM", mustWork = TRUE)
+ kenya_filepath <- system.file("extdata", "random_broken_colB.csv", package = "PvSTATEM", mustWork = TRUE)
- expect_warning(
- expect_error(read_data(kenya_filepath, verbose=FALSE))
- )
+ expect_error(read_data(kenya_filepath, verbose = FALSE))
})
diff --git a/vignettes/.gitignore b/vignettes/.gitignore
new file mode 100644
index 00000000..097b2416
--- /dev/null
+++ b/vignettes/.gitignore
@@ -0,0 +1,2 @@
+*.html
+*.R
diff --git a/vignettes/example_script.Rmd b/vignettes/example_script.Rmd
index 1ac5db3d..0197d753 100644
--- a/vignettes/example_script.Rmd
+++ b/vignettes/example_script.Rmd
@@ -7,6 +7,7 @@ vignette: >
%\VignetteIndexEntry{Simple example of basic PvSTATEM package pre-release version functionalities}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
+ %\VignetteDepends{ggplot2}
---
```{r setup, include=FALSE}
@@ -24,18 +25,15 @@ The basic functionality of the `PvSTATEM` package is reading raw MBA data. To pr
```{r}
library(PvSTATEM)
-plate_filepath <- system.file("extdata", "artificial_plate.csv", package = "PvSTATEM", mustWork = TRUE) # get the filepath of the csv dataset
+plate_filepath <- system.file("extdata", "random.csv", package = "PvSTATEM", mustWork = TRUE) # get the filepath of the csv dataset
plate <- read_data(plate_filepath) # read the data
-
```
After the plate is successfully loaded, we can look into some basic information about the plate.
```{r}
-
-
plate$summary()
plate$get_sample(1)
@@ -50,7 +48,6 @@ plate$analyte_names
## Warnings
Our scripts are designed to catch potential errors in the data. If there are any warnings, they will be stored in the `warnings` field of the plate object. The warnings can be accessed by the `$warnings` field of the plate object or by the `$warnings` field of the sample object.
-```{r}
```{r}
## warnings ----------------------------------------------------------------
@@ -72,6 +69,4 @@ plot_standard_curve_antibody(plate, antibody_name = "AMA1")
plate$blank_adjustment()
plot_standard_curve_antibody(plate, antibody_name = "AMA1")
-
-
```