In decusInLabore/biologicViewerSC: PKG_TITLE

The following R-script should allow you to create powerpoint presentations##

from your single-cell data.

For each slide, you can freely choose a title (Slidetitle). To make a plot,

go to the online single-cell Viewer, choose the plot you'd like to

incorporate in your presentation and use the bookmark button to generate

the required plotlink (figureLink). Each viewer requires the specification

of a few parameters which are given in the app-specific appParameterFile and

the pathToAppColorParameters file

Set the working directory to where you've copied the four files below or

adjust the paths to the correct location of those files, e.g. by doing

!!! You need to be inside the Crick or VPN connected to the Crick for the

following procedure to work !!!

setwd("/folder/where/you/have/copied/the/files/to")

Then we install required R-packages:

install.packages("remotes") remotes::install_github("decusInLabore/biologicSeqTools")

remotes::install_github("decusinlabore/biologicViewerSC")

Here are build-in example files for the Hpoly dataset:

here: https://shiny-bioinformatics.crick.ac.uk/shiny/boeings/EGCsHPoly_app

appParameterFile_Hpoly <- system.file("extdata/examples/Hpoly.db.txt",package = "biologicViewerSC") pathToAppColorParameters_Hpoly <- system.file("extdata/examples/Hpoly.colorParameters.txt",package = "biologicViewerSC")

Here are build-in example files for the Ifng dataset:

here: https://shiny-bioinformatics.crick.ac.uk/shiny/boeings/GliaIfngrKO_app

appParameterFile_WT_MT_infected <- system.file("extdata/examples/WT_MT_infected.db.txt",package = "biologicViewerSC") pathToAppColorParameters_WT_MT_infected <- system.file("extdata/examples/WT_MT_infected.colorParameters.txt",package = "biologicViewerSC")

Add as many items to the Slidelist as you'd like to have slides in your

presentation

slideList <- list( "Slide1" = list( "Slidetitle" = "H Poly Expression UMAP Ifngr1", "figureLink" = "https://shiny-bioinformatics.crick.ac.uk/shiny/boeings/EGCsHPoly_app/?inputs&gene=%22Ifngr1%22&lowColor=%22%23D3D3D3%22&y_axis=%22UMAP_2%22&dotcolor=%22%2300008B%22&showPlotLegend=true&splitByColumn=%22all%22&x_axis=%22UMAP_1%22&colorBy=%22lg10Expr%22&background=%22white%22&dotsize=1", "appParameterFile" = appParameterFile_Hpoly, "pathToAppColorParameters" = pathToAppColorParameters_Hpoly ), "Slide2" = list( "Slidetitle" = "A UMAP Test Plot", "figureLink" = "https://shiny-bioinformatics.crick.ac.uk/shiny/boeings/GliaIfngrKO_app/?inputs&gene=%22S100b%22&lowColor=%22%23D3D3D3%22&y_axis=%22UMAP_2%22&dotcolor=%22%2300008B%22&showPlotLegend=true&splitByColumn=%22all%22&x_axis=%22UMAP_1%22&colorBy=%22lg10Expr%22&background=%22white%22&dotsize=1", "appParameterFile" = appParameterFile_WT_MT_infected, "pathToAppColorParameters" = pathToAppColorParameters_WT_MT_infected ), "Slide3" = list( "Slidetitle" = "Another UMAP Test Plot", "figureLink" = "https://shiny-bioinformatics.crick.ac.uk/shiny/boeings/GliaIfngrKO_app/?inputs&MuscularisMacrophages3=%22%23FD7A63%22&Fibroblasts2=%22%23A0B915%22&lowColor=%22%23D3D3D3%22&SmoothMuscleCells=%22%2333D3A6%22&showPlotLegend=false&EndothelialCells2=%22%23E82F55%22&DendriticCells1=%22%2336DCB6%22&EpithelialCells=%22%23C48779%22&MonocyteMacrophages=%22%23EE7A6F%22&DendriticCells2=%22%23A67066%22&y_axis=%22UMAP_2%22&MuscularisMacrophages2=%22%23B706DC%22&dotcolor=%22%2300008B%22&MuscularisMacrophages4=%22%2361BBC6%22&NaturalKillerCells=%22%23621934%22&TCells1=%22%230351B5%22&dotsize=1&colorBy=%22ClusterName%22&CyclingMacrophages=%22%23C6B1F5%22&gene=%22S100b%22&EndothelialCells1=%22%23927E75%22&MesothelialCells2=%22%2335D156%22&EntericGliaCells=%22%23447BE9%22&Fibroblasts1=%22%23A91CC3%22&MesothelialCells1=%22%231069DF%22&MesothelialCells5=%22%23628D55%22&TCells3=%22%23DEA93F%22&OtherLymphoidCells=%22%234412C1%22&InterstitialCellsOfCajal=%22%23F1CB7A%22&Pericytes=%22%23E5AA42%22&MuscularisMacrophages1=%22%237FC9E4%22&splitByColumn=%22all%22&Bcells=%22%23576825%22&MesothelialCells4=%22%23AFC858%22&x_axis=%22UMAP_1%22&background=%22white%22&LymphaticEndothelialCells=%22%235F994B%22&MesothelialCells3=%22%232DA5D6%22&Neutrophils=%22%23203E53%22&TCells2=%22%2362841F%22", "appParameterFile" = appParameterFile_WT_MT_infected, "pathToAppColorParameters" = pathToAppColorParameters_WT_MT_infected ), "Slide4" = list( "Slidetitle" = "A UMAP Plot 3", "figureLink" = "https://shiny-bioinformatics.crick.ac.uk/shiny/boeings/GliaIfngrKO_app/?inputs&MuscularisMacrophages3=%22%23FD7A63%22&Fibroblasts2=%22%23A0B915%22&lowColor=%22%23D3D3D3%22&SmoothMuscleCells=%22%2333D3A6%22&showPlotLegend=false&EndothelialCells2=%22%23E82F55%22&DendriticCells1=%22%2336DCB6%22&EpithelialCells=%22%23C48779%22&MonocyteMacrophages=%22%23EE7A6F%22&DendriticCells2=%22%23A67066%22&y_axis=%22tSNE_2%22&MuscularisMacrophages2=%22%23B706DC%22&dotcolor=%22%2300008B%22&MuscularisMacrophages4=%22%2361BBC6%22&NaturalKillerCells=%22%23621934%22&TCells1=%22%230351B5%22&dotsize=1&colorBy=%22ClusterName%22&CyclingMacrophages=%22%23C6B1F5%22&gene=%22S100b%22&EndothelialCells1=%22%23927E75%22&MesothelialCells2=%22%2335D156%22&EntericGliaCells=%22%23447BE9%22&Fibroblasts1=%22%23A91CC3%22&MesothelialCells1=%22%231069DF%22&MesothelialCells5=%22%23628D55%22&TCells3=%22%23DEA93F%22&OtherLymphoidCells=%22%234412C1%22&InterstitialCellsOfCajal=%22%23F1CB7A%22&Pericytes=%22%23E5AA42%22&MuscularisMacrophages1=%22%237FC9E4%22&splitByColumn=%22genotype%22&Bcells=%22%23576825%22&MesothelialCells4=%22%23AFC858%22&x_axis=%22tSNE_1%22&background=%22white%22&LymphaticEndothelialCells=%22%235F994B%22&MesothelialCells3=%22%232DA5D6%22&Neutrophils=%22%23203E53%22&TCells2=%22%2362841F%22", "appParameterFile" = appParameterFile_WT_MT_infected, "pathToAppColorParameters" = pathToAppColorParameters_WT_MT_infected ), "Slide5" = list( "Slidetitle" = "A UMAP Plot 4", "figureLink" = "https://shiny-bioinformatics.crick.ac.uk/shiny/boeings/GliaIfngrKO_app/?inputs&MuscularisMacrophages3=%22%23FD7A63%22&Fibroblasts2=%22%23A0B915%22&lowColor=%22%23D3D3D3%22&SmoothMuscleCells=%22%2333D3A6%22&showPlotLegend=false&EndothelialCells2=%22%23E82F55%22&DendriticCells1=%22%2336DCB6%22&EpithelialCells=%22%23C48779%22&MonocyteMacrophages=%22%23EE7A6F%22&DendriticCells2=%22%23A67066%22&y_axis=%22Densityplot%22&MuscularisMacrophages2=%22%23B706DC%22&dotcolor=%22%2300008B%22&MuscularisMacrophages4=%22%2361BBC6%22&NaturalKillerCells=%22%23621934%22&TCells1=%22%230351B5%22&dotsize=1&colorBy=%22ClusterName%22&CyclingMacrophages=%22%23C6B1F5%22&gene=%22Malat1%22&EndothelialCells1=%22%23927E75%22&MesothelialCells2=%22%2335D156%22&EntericGliaCells=%22%23447BE9%22&Fibroblasts1=%22%23A91CC3%22&MesothelialCells1=%22%231069DF%22&MesothelialCells5=%22%23628D55%22&TCells3=%22%23DEA93F%22&OtherLymphoidCells=%22%234412C1%22&InterstitialCellsOfCajal=%22%23F1CB7A%22&Pericytes=%22%23E5AA42%22&MuscularisMacrophages1=%22%237FC9E4%22&splitByColumn=%22genotype%22&Bcells=%22%23576825%22&MesothelialCells4=%22%23AFC858%22&x_axis=%22lg10Expr%22&background=%22white%22&LymphaticEndothelialCells=%22%235F994B%22&MesothelialCells3=%22%232DA5D6%22&Neutrophils=%22%23203E53%22&TCells2=%22%2362841F%22", "appParameterFile" = appParameterFile_WT_MT_infected, "pathToAppColorParameters" = pathToAppColorParameters_WT_MT_infected ) )

The function below will generate a powerpoint presentation under the name

specified in the outputfile in your working directory.

biologicViewerSC::createPowerpointPresentation( slideList = slideList, outputfile="singleCell.powerpoint.presentation.pptx" )

decusInLabore/biologicViewerSC documentation built on Nov. 29, 2024, 11:46 a.m.