How to plot a matrix with user-chosen parameters? R Shiny - r

Question

I am trying to make a Shiny app that will plot gene of interest for a chosen patient. Each row is the gene name, and each column is a patient ID. For example:
99901 99902 99903 99904
SKI 4.789 5.789 6.324 1.2222
VWA1 6.901 7.002 5.89 4.567
TTLL10 6.783 7.345 8.987 6.345
library(shiny)
library(shinythemes)
library(lattice)
anno <- as.matrix(anno_genExp_gen3[1:3, 1:3])
#Define UI
ui <- fluidPage(
sidebarPanel(
titlePanel(title = "Gen3 Gene Expression Data"),
selectInput(inputId = "patients",
label = strong("Please choose patient/s to examine"),
choices = colnames(anno_genExp_off[,1:25]),
multiple = TRUE),
selectInput(inputId = "geneExp",
label = "Please select gene expressions/s to examine",
choices = rownames(anno_genExp_off[1:25,]),
multiple = TRUE)),
mainPanel(plotOutput("testPlot"))
)
server <- function(input, output) {
pdata <- reactive(input$patients)
gdata <-reactive(input$geneExp)
output$testPlot <- renderPlot ({
levelplot(anno,
col.regions=colorRampPalette(c("red","green","blue")))
})
}
shinyApp(ui = ui, server = server)
The code above just plots a small matrix, but how do I get it to plot user inputs using reactivity?
If the user chooses SKI and TTlLL10 only for patient 99901, how will I go about plotting this?

Answer 1

I've myself created a sample dataframe as you mentioned above. Here's the modified code.
Changes i made:
input$geneExp and input$patients are already reactive so there is no need to use a separate reactive function.
Filtered the dataframe for plotting use the same
Also, made a default selected value in the selectInput to avoid the initial error message when nothing is selected
library(shiny)
library(shinythemes)
library(lattice)
anno_genExp_off <- data.frame(`99901` = c(4.3,6.5,6.6),
`99902` = c(5.3,7.5,8.6),
`99903` = c(6.3,8.5,9.6),
row.names = c("SKI","VWA1","TTLL10"))
anno <- as.matrix(anno_genExp_off)
#Define UI
ui <- fluidPage(
sidebarPanel(
titlePanel(title = "Gen3 Gene Expression Data"),
selectInput(inputId = "patients",
label = strong("Please choose patient/s to examine"),
choices = colnames(anno_genExp_off),
selected = colnames(anno_genExp_off)[1],
multiple = TRUE),
selectInput(inputId = "geneExp",
label = "Please select gene expressions/s to examine",
choices = rownames(anno_genExp_off),
selected = rownames(anno_genExp_off)[1],
multiple = TRUE)),
mainPanel(plotOutput("testPlot"))
)
server <- function(input, output) {
#pdata <- reactive(input$patients)
#gdata <-reactive(input$geneExp)
output$testPlot <- renderPlot ({
levelplot(x = as.matrix(anno_genExp_off[which(rownames(anno_genExp_off) %in% input$geneExp) ,input$patients]),
col.regions=colorRampPalette(c("red","green","blue")))
})
}
shiny::shinyApp(ui,server)