#'name create_filtered_plot
create_filtered_plot <- function(dataset,filter_name,filter_value)
{
requireNamespace('ggplot2')
requireNamespace('qvalue')
pathway_description=0
a2=0
qvalue=qvalue::qvalue(round(dataset$pvalue,digits=5))$qvalue
Results = cbind(dataset,qvalue=qvalue)
Link1 = "http://rest.kegg.jp/list/pathway"
Table1 = readLines(Link1)
Table2 = t(data.frame(strsplit(Table1,'\t')))
Table3 = cbind(map_numbers = as.character(Table2[,1]),
pathway_description = as.character(Table2[,2]))
Table4 = gsub('path:map','',Table3)
Table5 = data.frame(Table4)
Table6 = merge(Table5,Results,by="map_numbers")
a1 = paste0("a2 = Table6[Table6$",filter_name,filter_value,",]")
eval(parse(text=a1))
Table6 = a2
Rich_factor = round(
Table6$deg_gene_numbers/Table6$background_gene_numbers,digits=2)
p <- ggplot2::ggplot(Table6, ggplot2::aes(x = Rich_factor,
y = pathway_description))
p + ggplot2::geom_point(ggplot2::aes(colour = qvalue,size =
deg_gene_numbers))+ ggplot2::scale_colour_gradientn(
colours=c("blue","white","red"))
}
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