From be1df62ef5a44d48a67892236befd869387fe7c5 Mon Sep 17 00:00:00 2001 From: Constantin Zackl Date: Fri, 1 Dec 2023 19:27:19 +0100 Subject: [PATCH 1/3] updates --- R/SignatureExplorationPlots.R | 6 +++--- inst/webserver_setup/app/Dockerfile | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/SignatureExplorationPlots.R b/R/SignatureExplorationPlots.R index 4f293cf..255e4c5 100644 --- a/R/SignatureExplorationPlots.R +++ b/R/SignatureExplorationPlots.R @@ -44,7 +44,7 @@ plot_signatureGenesPerMethod <- function(signature_list, vjust = -1, family = "Helvetica", color = "black" ) + - geom_hline(yintercept = 0, size = 1, colour = "#333333") + + geom_hline(yintercept = 0, linewidth = 1, colour = "#333333") + theme_minimal() + theme(legend.position = "none") + ggplot2::scale_fill_manual(values = RColorBrewer::brewer.pal(8, color_palette)[1:length(names(signature_list))]) + @@ -93,7 +93,7 @@ plot_conditionNumberPerMethod <- function(signature_list, fontface = "bold", vjust = -1, color = "black", size = 7, family = "Helvetica" ) + - geom_hline(yintercept = 0, size = 1, colour = "#333333") + + geom_hline(yintercept = 0, linewidth = 1, colour = "#333333") + theme_minimal() + labs(x = "Method", y = "Kappa") + theme(legend.position = "none") + @@ -142,7 +142,7 @@ plot_meanEntropyPerMethod <- function(signature_list, fontface = "bold", vjust = -1, color = "black", size = 7, family = "Helvetica" ) + - geom_hline(yintercept = 0, size = 1, colour = "#333333") + + geom_hline(yintercept = 0, linewidth = 1, colour = "#333333") + theme_minimal() + labs(x = "Method", y = "Entropy") + theme(legend.position = "none") + diff --git a/inst/webserver_setup/app/Dockerfile b/inst/webserver_setup/app/Dockerfile index 19146fc..010f38e 100644 --- a/inst/webserver_setup/app/Dockerfile +++ b/inst/webserver_setup/app/Dockerfile @@ -32,7 +32,7 @@ RUN R -e "pak::pkg_install('omnideconv/omnideconv', dependencies=TRUE)" #RUN R -e "remotes::install_github('omnideconv/DeconvExplorer', dependencies=TRUE)" RUN R -e "pak::pkg_install('omnideconv/DeconvExplorer', dependencies=TRUE)" -RUN R -e "reticulate::install_miniconda()" # will not install automatically +RUN R -e "reticulate::install_miniconda(force=TRUE)" # will not install automatically RUN R -e "omnideconv::install_all_python()" From ab23aa64d7672545478b7e627711222b22d8662b Mon Sep 17 00:00:00 2001 From: Constantin Zackl Date: Fri, 1 Dec 2023 19:34:10 +0100 Subject: [PATCH 2/3] minor changes --- tests/testthat/test-DeconvExplorer.R | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/testthat/test-DeconvExplorer.R b/tests/testthat/test-DeconvExplorer.R index 18447ac..38de9f6 100644 --- a/tests/testthat/test-DeconvExplorer.R +++ b/tests/testthat/test-DeconvExplorer.R @@ -4,6 +4,7 @@ test_that("Shiny app is generated", { ) }) + test_that("Helper funcs", { internal_list <- returnSelectedDeconvolutions(c("momf"), deconv_list) expect_true( From b7e19a6aba1a064157fbf4ea3dc3b3857662c99e Mon Sep 17 00:00:00 2001 From: Constantin Zackl Date: Fri, 1 Dec 2023 19:52:39 +0100 Subject: [PATCH 3/3] updates --- DESCRIPTION | 3 ++- inst/webserver_setup/app/Dockerfile | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 45cebc4..997f1db 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -57,6 +57,7 @@ Suggests: knitr, rmarkdown, bookdown, - testthat (>= 3.0.0) + testthat (>= 3.0.0), + markdown VignetteBuilder: knitr Config/testthat/edition: 3 diff --git a/inst/webserver_setup/app/Dockerfile b/inst/webserver_setup/app/Dockerfile index 010f38e..65ef888 100644 --- a/inst/webserver_setup/app/Dockerfile +++ b/inst/webserver_setup/app/Dockerfile @@ -8,6 +8,7 @@ ARG GITHUB_PAT RUN apt-get update && apt-get install -y \ sudo \ pandoc \ + apt-utils \ #pandoc-citeproc \ libcurl4-gnutls-dev \ libcairo2-dev \