v1.0

examples/dmrplot.Rmd

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+---
+title: "dmrplot"
+runtime: shiny
+output: flexdashboard::flex_dashboard
+params:
+  meth: "waterpipe_Funnorm_2022-01-18.rda" 
+  dmrs: "report_SmokingStatus/Cigarette_2022-03-24.dmrs.csv"
+---
+
+```{r echo = FALSE, message = FALSE}
+#library(data.table)
+library(tidyverse)
+library(GenomicRanges)
+library(ggplot2)
+library(reshape2)
+library(RColorBrewer)
+```
+
+
+```{r echo = FALSE}
+load(params$meth)
+dmrs<-read_tsv(params$dmrs) %>% mutate(ID=paste0(seqnames, ":", start, "-", end))
+```
+
+Column {.sidebar}
+--------------------------------------------------
+
+<h4>Parameters</h4>
+
+```{r echo = FALSE}
+selectInput("group", "group", choices = colnames(sampleSheet), selected = 3, multiple = FALSE)
+selectInput("dmr", "dmr", choices = dmrs$ID, selected = 1, multiple = FALSE)
+```
+
+Column
+--------------------------------------------------
+
+```{r echo = FALSE, message = FALSE}
+renderPlot({
+  
+  #foo<-table[ grepl(input$gene,table$overlapping.genes), ]
+  cpgs<-dmrs %>% filter(ID==input$dmr) %>% pull(overlapping.sites) %>% strsplit(",") %>% unlist()
+  colnames(betas)<-sampleSheet$samples
+  foo<-betas[cpgs,] %>% data.frame() %>% rownames_to_column("cpg") %>% 
+    gather("samples","betas",1:ncol(betas)+1) %>%
+    merge(sampleSheet,by="samples") %>%
+    group_by_at(c(input$group,"cpg")) %>%
+    filter(!is.na(betas)) %>%
+    summarise(sd=sd(betas),betas=mean(betas), .groups = "drop")
+  
+  ggplot(foo, aes(x=cpg, y=betas, ymin=(betas-sd/2), ymax=(betas+sd/2) , group=get(input$group), fill=get(input$group) )   ) +
+    geom_line() + 
+    geom_point() +
+    geom_ribbon(alpha=0.5) +
+    theme(axis.text.x=element_text(angle=50,hjust=1, size=10)) +
+    labs(fill=input$group) +
+    ggtitle(input$dmr)
+})
+```