Created
August 13, 2024 10:53
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use EBImage to explore spatial transcriptomics data
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| library(EBImage) | |
| library(shiny) | |
| ui = fluidPage( | |
| sidebarLayout( | |
| sidebarPanel( | |
| helpText("EBImage explorer"), | |
| fileInput("inimg", "file"), | |
| numericInput("scalefactor", "multfac", min=1, max=50, value=10,step=1), | |
| sliderInput("blursig", "sigma for blur", min=1, max=100, value=50) | |
| ), | |
| mainPanel( | |
| tabsetPanel( | |
| tabPanel("basic", plotOutput("basic")), | |
| tabPanel("blur", plotOutput("blurred")), | |
| tabPanel("clip", uiOutput("slider1"), uiOutput("slider2"), | |
| plotOutput("clipped")), | |
| tabPanel("about", verbatimTextOutput("vers")) | |
| ) | |
| ) | |
| ) | |
| ) | |
| server=function(input, output) { | |
| getImg = reactive({ | |
| validate(need(nchar(input$inimg)>0, "pick img")) | |
| EBImage::readImage( input$inimg$datapath ) | |
| }) | |
| output$basic = renderPlot({ | |
| img = getImg() | |
| display(img*input$scalefactor, method="raster") | |
| }) | |
| output$blurred = renderPlot({ | |
| img = getImg() | |
| display( gblur(img*input$scalefactor, sigma=input$blursig), method="raster") | |
| }) | |
| output$slider1 = renderUI({ | |
| img = getImg() | |
| d = dim(img) | |
| maxx = d[1] | |
| maxy = d[2] | |
| sliderInput("xsel", "xlim", min=1, max=maxx, value=c(1, maxx)) | |
| }) | |
| output$slider2 = renderUI({ | |
| img = getImg() | |
| d = dim(img) | |
| maxx = d[1] | |
| maxy = d[2] | |
| sliderInput("ysel", "ylim", min=1, max=maxy, value=c(1, maxy)) | |
| }) | |
| output$clipped = renderPlot({ | |
| img = getImg() | |
| validate(need(length(input$xsel)>0, "use slider")) | |
| display( input$scalefactor*img[ seq(input$xsel[1], input$xsel[2]), seq(input$ysel[1], input$ysel[2]) ], | |
| method="raster" ) | |
| }) | |
| } | |
| runApp(list(ui=ui, server=server)) |
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