Dear I've had problem with running R code. I've used monocles for my out-put plots (e.g. cluster plot and violin one).
It runs pretty fast (~ 20-40 sec) with loading data and executing cluster plot even with the user interaction command (which allows user can choose/change specific gene/marker she/he wants to express in cluster plot). However, it takes ~7 min to display the plots with ONLY ONE extra command: plot_gene_violin function/command? Could you guys help me with it? Is there any wrong with my code???? I've appreciated yours help a lot.
Thanks and best, NT
Here is server.R code which includes cluster plot and violin plot commands
(I can upload the whole code if it is necessary).
server <- function(input, output, session) {
output$plot_cell_clusters1<-renderPlot(
plot_cell_clusters (cds_all495Cells, color_by="Cluster", cell_size = 2.0))
output$plot_cell_clusters2<-renderPlot(
plot_cell_clusters(cds_all495Cells, cell_size = 2, color_by = "FACScellType"))
output$plot_cell_clusters3 <-renderPlot({
updateSelectInput(session, inputId='genes', label='please enter you marker', selected = NULL)
validate(need(input$genes == disp_table$gene_id, "A chosen gene is not found/type your gene"))
plot_cell_clusters (cds_all495Cells, markers=input$genes, cell_size = 3.0) +
scale_colour_gradient2(low = "#999999", mid = "lightblue", high = "darkblue", midpoint = 1.5, limits = c(-1, 4))
})
output$plot4<-renderPlot(
plot_genes_violin(cds_all495Cells, color_by= "Cluster", grouping = "Cluster", panel_order = input$genes))
}