comparison mutational_patterns.R @ 10:59c0e2a7965c draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 533394bd219d56cde7fb9721803e8aed8fd5a25d"

9:4ff3c984523b

             worklist[[i]] <- worklist[[i]][order(worklist[[i]][ ,"sum"], decreasing = T), ]
             worklist[[i]] <- worklist[[i]][1:opt$signum,]
             worklist[[i]] <- worklist[[i]][ , -length(as.data.frame(worklist[[i]]))]
        }
        worklist <- as.data.frame(melt(worklist))
        worklist[,2] <- paste0(worklist[,2], " - ", worklist[,4])
        head(worklist)
    }
    
    colnames(worklist) <- c("signature", "sample", "value", "level")
    worklist <- as.data.frame(worklist %>% group_by(sample) %>% mutate(value=value/sum(value)*100))

    worklist$label <- factor(worklist$signature)
    worklist$signature <- factor(worklist$signature)
    p7 <-  ggplot(worklist, aes(x="", y=value, group=signature, fill=signature)) +
              geom_bar(width = 1, stat = "identity") +
              geom_text(aes(label = label), position = position_stack(vjust = 0.5), color="black", size=3) +
              coord_polar("y", start=0) + facet_wrap(~ sample) +
              labs(x="", y="Samples", fill = cosmic_tag) +
              scale_fill_manual(name = paste0(opt$signum, " most contributing\nsignatures\n(in each label/tissue)"),
                                values = cosmic_colors[as.numeric(levels(factor(worklist$label)))]) +
              theme(axis.text = element_blank(),
                    axis.ticks = element_blank(),

10:59c0e2a7965c

             worklist[[i]] <- worklist[[i]][order(worklist[[i]][ ,"sum"], decreasing = T), ]
             worklist[[i]] <- worklist[[i]][1:opt$signum,]
             worklist[[i]] <- worklist[[i]][ , -length(as.data.frame(worklist[[i]]))]
        }
        worklist <- as.data.frame(melt(worklist))
        worklist[,2] <- paste0(worklist[,4], " - ", worklist[,2])
        head(worklist)
    }
    
    colnames(worklist) <- c("signature", "sample", "value", "level")
    worklist <- as.data.frame(worklist %>% group_by(sample) %>% mutate(value=value/sum(value)*100))

    worklist$label <- factor(worklist$signature)
    worklist$signature <- factor(worklist$signature)
    p7 <-  ggplot(worklist, aes(x="", y=value, group=signature, fill=signature)) +
              geom_bar(width = 1, stat = "identity") +
              geom_text(aes(label = label), position = position_stack(vjust = 0.5), color="black", size=3) +
              coord_polar("y", start=0) + facet_wrap(.~sample) +
              labs(x="", y="Samples", fill = cosmic_tag) +
              scale_fill_manual(name = paste0(opt$signum, " most contributing\nsignatures\n(in each label/tissue)"),
                                values = cosmic_colors[as.numeric(levels(factor(worklist$label)))]) +
              theme(axis.text = element_blank(),
                    axis.ticks = element_blank(),