From e20aba4570ca3caa9fc81569f0edcbbaf41e3ea9 Mon Sep 17 00:00:00 2001
From: Flavio Lombardo <flavio.lombardo@unibas.ch>
Date: Tue, 14 Jan 2025 18:39:37 +0100
Subject: [PATCH] Feedback received and applied
---
DESCRIPTION | 12 ++++++------
NAMESPACE | 1 +
R/get_QC_plots_and_stats.R | 6 +++---
R/parsers.R | 3 ++-
man/get_QC_plots_parsed_merged_data.Rd | 2 +-
man/string_parsing.Rd | 2 +-
tests/testthat/test_cases.R | 4 ++--
7 files changed, 16 insertions(+), 14 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 9c045b5..de1cc47 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,11 +1,11 @@
Package: drugsens
Title: Automated Analysis of 'QuPath' Output Data and Metadata Extraction
-Description: A comprehensive toolkit for analyzing microscopy data output from
- 'QuPath' software. Provides functionality for automated data processing,
- metadata extraction, and statistical analysis of imaging results.
- Designed to complement the STAR Protocol Protocol for quantifying drug
- sensitivity in 3D patient-derived ovarian cancer models
- <doi:10.1016/j.xpro.2024.103274>.
+Description: A comprehensive toolkit for analyzing microscopy data output from 'QuPath' software.
+ Provides functionality for automated data processing, metadata extraction, and statistical
+ analysis of imaging results. The methodology implemented in this package is based on
+ Labrosse et al. (2024) <doi:10.1016/j.xpro.2024.103274> "Protocol for quantifying drug
+ sensitivity in 3D patient-derived ovarian cancer models", which describes the complete
+ workflow for drug sensitivity analysis in patient-derived cancer models.
Version: 0.1.0
BugReports: https://git.scicore.unibas.ch/ovca-research/drugsens/-/issues
SystemRequirements: QuPathâ„¢ 4.0.0 or higher
diff --git a/NAMESPACE b/NAMESPACE
index 579ce91..1bec287 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,6 +7,7 @@ export(get_QC_plots)
export(get_QC_plots_parsed_merged_data)
export(make_count_dataframe)
export(make_run_config)
+export(string_parsing)
import(ggplot2)
import(ggpubr)
import(knitr)
diff --git a/R/get_QC_plots_and_stats.R b/R/get_QC_plots_and_stats.R
index 5571930..4daf74c 100644
--- a/R/get_QC_plots_and_stats.R
+++ b/R/get_QC_plots_and_stats.R
@@ -24,7 +24,7 @@
#' @examples
#' \dontrun{
#' qc <- get_QC_plots_parsed_merged_data(bind_data, save_plots = TRUE,
-#' save_list_of_plots = TRUE)
+#' save_list_of_plots = FALSE)
#' }
#' @export
@@ -64,8 +64,8 @@ get_QC_plots_parsed_merged_data <- function(.data,
if (!is.null(isolate_specific_drug)) subset_data <- subset_data[subset_data[[drug_column_name]] %in% isolate_specific_drug, ]
if (nrow(subset_data) < 1) {
- print(unique(subset_data[[PID_column_name]]))
- print(unique(subset_data[[drug_column_name]]))
+ message(unique(subset_data[[PID_column_name]]))
+ message(unique(subset_data[[drug_column_name]]))
stop("ERROR: Your filtering query has returned no observations")
}
diff --git a/R/parsers.R b/R/parsers.R
index bc0153f..034cac0 100644
--- a/R/parsers.R
+++ b/R/parsers.R
@@ -8,11 +8,12 @@
#' @importFrom stringr str_count
#' @return A `dataframe`/`tibble`.
#' @param .data dataframe with parsed metadata
+#' @export
#' @examples
#' input_data <- data.frame(
#' Image = "B516_Ascites_2023-11-25_DOC2020-12-14_dmso_rep_Ecad_cCasp3_(series 01).tif"
#' )
-#' test <- drugsens:::string_parsing(input_data)
+#' test <- drugsens::string_parsing(input_data)
#' \dontrun{
#' data.parsed <- string_parsing(.data)
#' }
diff --git a/man/get_QC_plots_parsed_merged_data.Rd b/man/get_QC_plots_parsed_merged_data.Rd
index 221cc7e..de2b2e5 100644
--- a/man/get_QC_plots_parsed_merged_data.Rd
+++ b/man/get_QC_plots_parsed_merged_data.Rd
@@ -56,6 +56,6 @@ This plot can show trends within the dataset and run some basic statistics.
\examples{
\dontrun{
qc <- get_QC_plots_parsed_merged_data(bind_data, save_plots = TRUE,
- save_list_of_plots = TRUE)
+ save_list_of_plots = FALSE)
}
}
diff --git a/man/string_parsing.Rd b/man/string_parsing.Rd
index e6b8843..1317c73 100644
--- a/man/string_parsing.Rd
+++ b/man/string_parsing.Rd
@@ -20,7 +20,7 @@ The metadata will be then associated to the count file as well
input_data <- data.frame(
Image = "B516_Ascites_2023-11-25_DOC2020-12-14_dmso_rep_Ecad_cCasp3_(series 01).tif"
)
-test <- drugsens:::string_parsing(input_data)
+test <- drugsens::string_parsing(input_data)
\dontrun{
data.parsed <- string_parsing(.data)
}
diff --git a/tests/testthat/test_cases.R b/tests/testthat/test_cases.R
index bb105ab..fbd7cf5 100644
--- a/tests/testthat/test_cases.R
+++ b/tests/testthat/test_cases.R
@@ -82,7 +82,7 @@ test_that("The parsing is working", {
ConcentrationUnits1 = "uM",
ConcentrationUnits2 = "nm",
Treatment_complete = "TreatmentRana10uM-15nm")
- expect_equal(drugsens:::string_parsing(input_data), expected = expected_output)
+ expect_equal(drugsens::string_parsing(input_data), expected = expected_output)
})
test_that("Another parsing test", {
@@ -101,7 +101,7 @@ test_that("Another parsing test", {
ConcentrationUnits1 = NA_character_,
ConcentrationUnits2 = NA_character_,
Treatment_complete = "dmso")
- expect_equal(drugsens:::string_parsing(input_data), expected = expected_output)
+ expect_equal(drugsens::string_parsing(input_data), expected = expected_output)
# Image1 <- "B516_Ascites_2023-11-25_DOC2020-12-14_CarboplatinPaclitaxel_100_uM_10_nM_Ecad_cCasp3_(series 01).tif"
# Image2 <- "A8759_Spleen_2020.11.10_DOC2001.10.05_compoundX34542_1000_uM_EpCAM_Ecad_cCasp3_(series 01).tif"
# Image3 <- "A8759_Spleen_2020.11.10_DOC2001.10.05_compoundX34542_1000_uM_EpCAM_Ecad_cCasp3_(series 01).tif"
--
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