diff --git a/DESCRIPTION b/DESCRIPTION index 4ee1a97..5024821 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -7,6 +7,14 @@ Authors@R: person( given = "Constantin", family = "Zackl", role = c("aut", "cre"), email = "zacklcon@uni-mainz.de", comment = c(ORCID = "0000-0003-1991-6943") + ), + person( + given = "Alexander", family = "Dietrich", role = c("aut"), + email = "alex.dietrich@tum.de", comment = c(ORCID = "0000-0002-8661-0453") + ), + person( + given = "Lorenzo", family = "Merotto", role = c("aut"), + email = "lorenzo.merotto@uibk.ac.at", comment = c(ORCID = "0009-0006-0637-8436") ), person( given = "Federico", family = "Marini", role = c("aut"), diff --git a/NAMESPACE b/NAMESPACE index 8c13c64..5cec841 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -18,7 +18,8 @@ export(returnSelectedDeconvolutions) export(selectGenesByScore) import(omnideconv) import(shiny, except = c(renderDataTable, dataTableOutput)) -import(shinyBS) +importFrom(BioQC,entropySpecificity) +importFrom(BioQC,gini) importFrom(ComplexHeatmap,Heatmap) importFrom(ComplexHeatmap,UpSet) importFrom(ComplexHeatmap,comb_size) @@ -56,6 +57,7 @@ importFrom(ggplot2,geom_rect) importFrom(ggplot2,geom_text) importFrom(ggplot2,geom_tile) importFrom(ggplot2,ggplot) +importFrom(ggplot2,ggsave) importFrom(ggplot2,guide_colorbar) importFrom(ggplot2,guides) importFrom(ggplot2,labs) @@ -67,6 +69,8 @@ importFrom(ggplot2,theme_minimal) importFrom(ggplot2,ylim) importFrom(ggpubr,stat_cor) importFrom(grDevices,colorRampPalette) +importFrom(grDevices,dev.off) +importFrom(grDevices,pdf) importFrom(grid,gpar) importFrom(grid,unit) importFrom(plotly,config) @@ -82,6 +86,7 @@ importFrom(rintrojs,readCallback) importFrom(rlang,.data) importFrom(shiny,addResourcePath) importFrom(shinyWidgets,actionBttn) +importFrom(shinyBS,bsPopover) importFrom(shinycssloaders,withSpinner) importFrom(shinydashboard,box) importFrom(shinydashboard,dashboardBody) @@ -100,7 +105,10 @@ importFrom(shinydashboard,valueBoxOutput) importFrom(shinyjs,hide) importFrom(shinyjs,show) importFrom(shinyjs,useShinyjs) +importFrom(stats,complete.cases) importFrom(stats,cor.test) +importFrom(stats,dist) +importFrom(stats,hclust) importFrom(stats,sd) importFrom(stringr,str_split) importFrom(stringr,str_to_title) @@ -109,3 +117,7 @@ importFrom(utils,read.delim) importFrom(utils,write.csv) importFrom(utils,write.table) importFrom(waiter,Waitress) +importFrom(waiter,waiter_hide) +importFrom(waiter,waiter_show) +importFrom(waiter,waiter_show_on_load) +importFrom(waiter,waiter_update) diff --git a/R/DeconvExplorer-pkg.R b/R/DeconvExplorer-pkg.R index 36215bb..2b3298d 100644 --- a/R/DeconvExplorer-pkg.R +++ b/R/DeconvExplorer-pkg.R @@ -13,22 +13,26 @@ #' geom_tile ggplot guide_colorbar guides labs scale_fill_gradient theme geom_text element_blank #' geom_hline scale_colour_brewer scale_fill_brewer ylim theme_minimal geom_rect element_rect #' @importFrom shinycssloaders withSpinner -#' @importFrom waiter Waitress +#' @importFrom waiter Waitress waiter_hide waiter_show waiter_show_on_load +#' waiter_update #' @importFrom rlang .data #' @importFrom rintrojs introBox introjs introjsUI readCallback -#' @importFrom DT datatable dataTableOutput renderDataTable formatRound formatPercentage +#' @importFrom DT datatable dataTableOutput renderDataTable formatRound +#' formatPercentage #' @importFrom shinyjs useShinyjs hide show #' @importFrom utils write.csv write.table read.delim #' @importFrom stringr str_to_title str_split #' @importFrom tidyr pivot_longer -#' @importFrom stats sd cor.test -#' @importFrom ComplexHeatmap Heatmap make_comb_mat UpSet comb_size upset_top_annotation extract_comb +#' @importFrom stats sd cor.test complete.cases dist hclust +#' @importFrom ComplexHeatmap Heatmap make_comb_mat UpSet comb_size +#' upset_top_annotation extract_comb #' @importFrom grid gpar unit -#' @importFrom InteractiveComplexHeatmap InteractiveComplexHeatmapOutput makeInteractiveComplexHeatmap +#' @importFrom InteractiveComplexHeatmap InteractiveComplexHeatmapOutput +#' makeInteractiveComplexHeatmap #' @importFrom RColorBrewer brewer.pal #' @importFrom circlize colorRamp2 #' @importFrom ggforce facet_grid_paginate -#' @importFrom grDevices colorRampPalette +#' @importFrom grDevices colorRampPalette dev.off pdf #' @importFrom ggpubr stat_cor #' @importFrom corrplot corrplot #' @importFrom SummarizedExperiment assays diff --git a/R/DeconvExplorer.R b/R/DeconvExplorer.R index ed6a586..8187b62 100644 --- a/R/DeconvExplorer.R +++ b/R/DeconvExplorer.R @@ -759,6 +759,13 @@ DeconvExplorer <- function(deconvexp_bulk = NULL, ) ) +refUnspecificPopover <- + shinyBS::bsPopover( + id = "refUnspecificQ", + title = "", + content = "The overall expression is binned into 'high', 'medium' and 'low expression' for each gene. The number of cell types the gene has to be in the 'high' bin can be modified and defaults to 1. Each gene expressed 'high' in more cell types than this parameter is removed. " + ) + refinementBestNBox <- shinydashboard::box( solidHeader = FALSE, width = NULL, background = "red", fluidRow( diff --git a/R/Global.R b/R/Global.R index 8d0fde6..1cc321a 100644 --- a/R/Global.R +++ b/R/Global.R @@ -29,7 +29,8 @@ returnSelectedDeconvolutions <- function(deconv_select, deconv_list) { #' Modal window to print error messages or other warnings #' -#' @param error_message +#' @param error_message Character string, with the content of the error to +#' display #' #' @return NULL #' @export diff --git a/R/zzz.R b/R/zzz.R index e9a4c8e..2153ae0 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -2,4 +2,4 @@ .onLoad <- function(libname, pkgname) { shiny::addResourcePath("sbs", system.file("www", package = "shinyBS")) -} \ No newline at end of file +} diff --git a/man/DeconvExplorer-pkg.Rd b/man/DeconvExplorer-pkg.Rd index d0e4a81..47586f5 100644 --- a/man/DeconvExplorer-pkg.Rd +++ b/man/DeconvExplorer-pkg.Rd @@ -21,6 +21,8 @@ Useful links: Authors: \itemize{ + \item Alexander Dietrich \email{your@email.here} (\href{https://orcid.org/0000-0002-8661-0453}{ORCID}) + \item Lorenzo Merotto \email{lorenzo.merotto@uibk.ac.at} (\href{https://orcid.org/0009-0006-0637-8436}{ORCID}) \item Federico Marini \email{marinif@uni-mainz.de} (\href{https://orcid.org/0000-0003-3252-7758}{ORCID}) } diff --git a/man/errorModal.Rd b/man/errorModal.Rd index 2b3c3de..aee2db2 100644 --- a/man/errorModal.Rd +++ b/man/errorModal.Rd @@ -7,7 +7,8 @@ errorModal(error_message = NULL) } \arguments{ -\item{error_message}{} +\item{error_message}{Character string, with the content of the error to +display} } \description{ Modal window to print error messages or other warnings diff --git a/tests/testthat/test-signatures.R b/tests/testthat/test-signatures.R index 2d540cd..a08428e 100644 --- a/tests/testthat/test-signatures.R +++ b/tests/testthat/test-signatures.R @@ -52,8 +52,4 @@ test_that("Signature refinement operations are correct", { max_count = 3, labels = c("A", "B", "C", "D") )) - - - entropy_calc <- scoreEntropy(signature_list$bisque[1, ]) - expect_true(is.numeric(entropy_calc)) })