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Download subRVIS data table and plot locally #3

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Download subRVIS data table and plot locally #3

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Yatros Sep 25, 2017
7cb4633
Merge pull request #1 from Yatros/Yatros-patch-1
Yatros Sep 25, 2017
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292 changes: 292 additions & 0 deletions server.R
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Original file line number Diff line number Diff line change
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library(shiny)
source("C:/Users/m119979/Desktop/subrvis-master/variant_plotting/src/geneplots.R")

## functions
Scores2Percentiles <- function(scores) {
stopifnot(is.numeric(scores))
return((rank(scores) / length(scores)) * 100)
}

# for domains
dmn.data <- ReadSubrgnData("C:/Users/m119979/Desktop/subrvis-master/variant_plotting/data/domains_table.txt")
dmn.data$perc <- Scores2Percentiles(dmn.data$subRVIS)
dmn.bed <- ReadSubrgnBed("C:/Users/m119979/Desktop/subrvis-master/variant_plotting/data/domains.bed")
dmn.map <- ReadDomainMap("C:/Users/m119979/Desktop/subrvis-master/variant_plotting/data/cdd_table.txt")
dmn.pvals <- ReadGenePvals("C:/Users/m119979/Desktop/subrvis-master/variant_plotting/data/domains_gene_pvals.txt")
dmn.sds <- ReadGeneSds("C:/Users/m119979/Desktop/subrvis-master/variant_plotting/data/domains_gene_sds.txt")

# for exons
exn.data <- ReadSubrgnData("C:/Users/m119979/Desktop/subrvis-master/variant_plotting/data/exons_table.txt")
exn.data$perc <- Scores2Percentiles(exn.data$subRVIS)
exn.bed <- ReadSubrgnBed("C:/Users/m119979/Desktop/subrvis-master/variant_plotting/data/exons.bed")
exn.map <- NULL
exn.pvals <- ReadGenePvals("C:/Users/m119979/Desktop/subrvis-master/variant_plotting/data/exons_gene_pvals.txt")
exn.sds <- ReadGeneSds("C:/Users/m119979/Desktop/subrvis-master/variant_plotting/data/exons_gene_sds.txt")

# for all
strand.map <- ReadStrandData("C:/Users/m119979/Desktop/subrvis-master/variant_plotting/data/strand_data.txt")

# Define server logic
shinyServer(function(input, output) {

# Expression that generates the plot. The expression is
# wrapped in a call to renderPlot to indicate that:
#
# 1) It is "reactive" and therefore should re-execute automatically
# when inputs change
# 2) Its output type is a plot

GetGene <- eventReactive(input$plot, {
input$gene
})

GetRgn <- eventReactive(input$plot, {
input$rgn
})

GetScoreType <- eventReactive(input$plot, {
input$score.type
})


GetVariants <- eventReactive(input$plot, {

if (is.null(input$variants) || input$variants == "") {
return(NULL)
}


variants <- tryCatch({
read.table(textConnection(input$variants), header=F)
}, error=function(e) {
stop("Unrecognized format for variants.")
})

if (ncol(variants) != 2) {
stop("Variants should have two columns: chromosome and position.")
}


colnames(variants) <- c("chrom", "pos")
if (!is.numeric(variants$pos)){
stop("Variant position should be numeric.")
}

return(variants)
})

GetPlotData <- eventReactive(input$plot, {
rgn <- GetRgn()
score.type <- GetScoreType()

if (rgn == "Domains") {
subrgn.data <- dmn.data
subrgn.bed <- dmn.bed
subrgn.map <- dmn.map
gene.pvals <- dmn.pvals
gene.sds <- dmn.sds
} else {
subrgn.data <- exn.data
subrgn.bed <- exn.bed
subrgn.map <- exn.map
gene.pvals <- exn.pvals
gene.sds <- exn.sds
}

gene <- GetGene()
if (!(toupper(gene) %in% toupper(subrgn.data$gene))) {
err.msg <- paste("Gene", gene, "cannot be found.")
stop(err.msg)
}

strand <- strand.map[toupper(rownames(strand.map)) == toupper(gene), ]
if((length(strand) != 1) || (!(strand %in% c("+", "-")))) {
err.msg <- paste("Gene", gene, "has no strand data.")
stop(err.msg)
}


variants <- GetVariants()

gene.subrgns <- GetGeneSubrgn(subrgn.data, subrgn.bed, subrgn.map, gene, rgn, score.type)
gene.name <- unique(gene.subrgns$gene)
stopifnot(length(gene.name)==1)

p.val <- gene.pvals[toupper(gene.name), ]
gene.sd <- gene.sds[toupper(gene.name), "percentile"]
gene.bed <- subrgn.bed[toupper(subrgn.bed$gene) == toupper(gene), ]

return(list(gene.subrgns = gene.subrgns,
subrgn.bed = subrgn.bed,
gene.bed = gene.bed,
gene.name = gene.name,
p.val = p.val,
gene.sd = gene.sd,
variants = variants,
rgn = rgn,
score.type = score.type,
strand = strand))
})


output$genePlot <- renderPlot({

plot.data <- GetPlotData()

gene.plot <- PlotGeneSkel(plot.data$gene.subrgns, plot.data$gene.name, plot.data$rgn, plot.data$score.type)

gene.plot <- PlotConnectors(gene.plot, plot.data$gene.subrgns, plot.data$strand)
if (plot.data$strand == "-") {
gene.plot <- gene.plot + scale_x_reverse(label=function(x) -(x-max(plot.data$gene.subrgns$end)))
}

if (!is.null(plot.data$variants)) {
gene.plot <- AddVariants(gene.plot, plot.data$gene.subrgns, plot.data$subrgn.bed, plot.data$variants, plot.data$strand)
}

ylab.txt <- ifelse(plot.data$score.type=="Percentiles", "subRVIS Percentile", "subRVIS Raw Score")
plot(gene.plot + labs(x=paste0("Gene Position\n",
"subRVIS P-value for known pathogenic mutations: ",
round(plot.data$p.val, digits=3),
"\nsubRVIS SDP: ",
round(plot.data$gene.sd, digits=1),
"%"),
y=ylab.txt))
})

output$var.table = renderDataTable({
plot.data <- GetPlotData()

plot.table <- plot.data$gene.subrgns
plot.table$var.count <- rep(0, nrow(plot.table))

gene.chrom <- unique(plot.data$gene.bed$chrom)
stopifnot(length(gene.chrom) == 1)

variants <- plot.data$variants
variants <- variants[variants$chrom == gene.chrom, ]

positions <- variants$pos - 1 # convert to 0-based BED coords

for (pos in positions) {
subrgn.name <- plot.data$gene.bed[pos >= plot.data$gene.bed$start & pos < plot.data$gene.bed$end, "subrgn"]
stopifnot(length(subrgn.name) <= 1)

if(length(subrgn.name) == 1) {
plot.table[subrgn.name, "var.count"] <- plot.table[subrgn.name, "var.count"] + 1
}

}

plot.table$name <- rownames(plot.table)

cols.to.plot <- c("name", "start", "end", "size", "coverage_percent", "subRVIS", plot.data$rgn, "var.count")

plot.table <- plot.table[, cols.to.plot]
plot.table$start <- plot.table$start + 1

if((plot.data$strand == "-") && (nrow(plot.table) != 1)) {
# Need to reverse coordinates
plot.table <- plot.table[order(-plot.table$start), ]
plot.table$start[1] <- 1
plot.table$end[1] <- plot.table$size[1]
for (i in 2:nrow(plot.table)) {
plot.table[i, "start"] <- plot.table$end[i-1] + 1
plot.table$end[i] <- plot.table$size[i] + plot.table$start[i] - 1
}
}

colnames(plot.table) <- c("name", "start", "end", "size",
"percent_covered", "score",
"sub-region", "variant_count")

return(plot.table)
})

output$downloadData <- downloadHandler(
filename = function() {
paste('subRVIS table','.csv', sep='')
},
content = function(file){
plot.data <- GetPlotData()

plot.table <- plot.data$gene.subrgns
plot.table$var.count <- rep(0, nrow(plot.table))

gene.chrom <- unique(plot.data$gene.bed$chrom)
stopifnot(length(gene.chrom) == 1)

variants <- plot.data$variants
variants <- variants[variants$chrom == gene.chrom, ]

positions <- variants$pos - 1 # convert to 0-based BED coords

for (pos in positions) {
subrgn.name <- plot.data$gene.bed[pos >= plot.data$gene.bed$start & pos < plot.data$gene.bed$end, "subrgn"]
stopifnot(length(subrgn.name) <= 1)

if(length(subrgn.name) == 1) {
plot.table[subrgn.name, "var.count"] <- plot.table[subrgn.name, "var.count"] + 1
}

}

plot.table$name <- rownames(plot.table)

cols.to.plot <- c("name", "start", "end", "size", "coverage_percent", "subRVIS", plot.data$rgn, "var.count")

plot.table <- plot.table[, cols.to.plot]
plot.table$start <- plot.table$start + 1

if((plot.data$strand == "-") && (nrow(plot.table) != 1)) {
# Need to reverse coordinates
plot.table <- plot.table[order(-plot.table$start), ]
plot.table$start[1] <- 1
plot.table$end[1] <- plot.table$size[1]
for (i in 2:nrow(plot.table)) {
plot.table[i, "start"] <- plot.table$end[i-1] + 1
plot.table$end[i] <- plot.table$size[i] + plot.table$start[i] - 1
}
}

colnames(plot.table) <- c("name", "start", "end", "size",
"percent_covered", "score",
"sub-region", "variant_count")

table_data <- plot.table

write.csv(table_data, file)
})


output$downloadPlot <- downloadHandler(
filename = function() {
paste("subRVIS plot", ".svg", sep='')
},
content = function(file) {
plot.data <- GetPlotData()

gene.plot <- PlotGeneSkel(plot.data$gene.subrgns, plot.data$gene.name, plot.data$rgn, plot.data$score.type)

gene.plot <- PlotConnectors(gene.plot, plot.data$gene.subrgns, plot.data$strand)
if (plot.data$strand == "-") {
gene.plot <- gene.plot + scale_x_reverse(label=function(x) -(x-max(plot.data$gene.subrgns$end)))
}

if (!is.null(plot.data$variants)) {
gene.plot <- AddVariants(gene.plot, plot.data$gene.subrgns, plot.data$subrgn.bed, plot.data$variants, plot.data$strand)
}

ylab.txt <- ifelse(plot.data$score.type=="Percentiles", "subRVIS Percentile", "subRVIS Raw Score")

plot(gene.plot + labs(x=paste0("Gene Position\n",
"subRVIS P-value for known pathogenic mutations: ",
round(plot.data$p.val, digits=3),
"\nsubRVIS SDP: ",
round(plot.data$gene.sd, digits=1),
"%"),
y=ylab.txt))

ggsave(file, plot = last_plot (), dpi = 300, width = 12, height = 6, units = "in")
})
})
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