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b/c_VisualizationScript/Visulz_bulkRNA_volcano.R |
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# MESSAGE ----------------------------------------------------------------- |
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# |
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# author: Yulin Lyu |
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# email: lvyulin@pku.edu.cn |
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# |
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# require: R whatever |
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# |
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# --- |
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# 1. Load packages -------------------------------------------------------- |
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setwd("exampleData/RNA") |
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# grammar |
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library(tidyverse) |
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library(magrittr) |
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library(glue) |
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library(data.table) |
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# analysis |
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library(DESeq2) |
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# graphics |
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library(ggplot2) |
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library(ggrepel) |
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library(ggsci) |
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library(scales) |
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library(latex2exp) |
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# 2. Load data ------------------------------------------------------------ |
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diffData <- fread("mid/ES_vs_Fib.DEG.csv") |
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colnames(diffData)[1] <- "gene" |
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diffData[is.na(padj), padj := 1][] |
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diffData[, p := -log10(padj)][] |
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# 3. Plot ----------------------------------------------------------------- |
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diffData[, type := "ns"][] |
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diffData[log2FoldChange > 3 & padj < 0.05, type := "up"][log2FoldChange < -3 & padj < 0.05, type := "down"][] |
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labelGene <- diffData[order(p, decreasing = T)][type == "up"][1:10] |
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pal_nejm()(8) %>% show_col() |
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typeColor <- structure( |
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c(pal_nejm()(2), "gray80"), |
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names = c("up", "down", "ns") |
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) |
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ggplot(diffData, aes(x = log2FoldChange, y = p)) + |
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geom_point(aes(color = type, size = p), show.legend = F) + |
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geom_hline(yintercept = -log10(0.05), color = "gray60", linetype = "dashed") + |
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geom_vline(xintercept = 3, color = "gray60", linetype = "dashed") + |
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geom_vline(xintercept = -3, color = "gray60", linetype = "dashed") + |
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geom_text_repel( |
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data = labelGene, aes(label = gene), |
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size = 3, fontface = "italic", |
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nudge_x = .5, nudge_y = .5, |
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max.overlaps = 100) + |
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scale_radius(range = c(.1, 2)) + |
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scale_color_manual(values = typeColor) + |
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scale_y_continuous(expand = expansion(c(0, 0.05))) + |
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labs( |
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x = TeX("$log_{2}(Fold\\,Change)$"), |
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y = TeX("$-log_{10}(\\textit{P}\\,value)$")) + |
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theme( |
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aspect.ratio = 1, |
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panel.background = element_blank(), |
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panel.grid = element_blank(), |
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axis.line = element_line() |
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) |
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ggsave("plot/ES_vs_Fib.volcano.pdf", width = 4, height = 4) |