【简单热图】
# 调用下载的pheatmap包。 library(pheatmap)#设置当前工作目录，setwd("目标路径")即保存待测文件的目录，使R能够调用。 setwd("C:/Users/81927/Desktop") # exp,样品表达量；cellwidth，热图每格宽度；cellheight，热图每格高度； # cluster_cols，对列进行聚类；cluster_rows，对行进行聚类； exppheatmap(exp,cellwidth = 20,cellheight = 10, cluster_cols = T, cluster_rows = T)
# 对表达量取以2为底的对数 pheatmap(log((exp+1),2),cellwidth = 20,cellheight = 10,cluster_cols = T,cluster_rows = T)# 更换热图颜色，colorRampPalette函数支持自定义的创建一系列的颜色梯度。pheatmap(log((exp+1),2),cellwidth=20, cellheight=10, cluster_cols=F, cluster_rows=T, color=colorRampPalette(c("navy","white","red"))(10))
【简单火山图】# 无标注火山图
# 火山图数据包含四列，genename、log2FoldChange、pvalue、padj# 调用下载的ggplot2包 library(ggplot2)# 一个展示基因差异表达水平的火山图示例 gene # 例如这里自定义根据 |log2FoldChange| >= 1 和 pvalue < 0.01标记差异类型 gene[which(gene$pvalue < 0.01 & gene$log2FoldChange <= -1),'sig'] gene[which(gene$pvalue < 0.01 & gene$log2FoldChange >= 1),'sig']gene[which(gene$pvalue >= 0.01 | abs(gene$log2FoldChange) < 1),'sig']
# 横轴 log2FoldChange，纵轴 -log10(pvalue)，颜色表示差异 p geom_point(alpha = 0.6, size = 1) + scale_colour_manual(values = c('red2', 'blue2', 'gray'), limits =c('Up', 'Down', 'None')) + theme(panel.grid = element_blank(),panel.background = element_rect(color = 'black', fill = 'transparent'),plot.title = element_text(hjust = 0.5)) + theme(legend.key = element_rect(fill ='transparent'), legend.background = element_rect(fill = 'transparent'),legend.position = c(0.9, 0.93)) + geom_vline(xintercept = c(-1, 1), color ='gray', size = 0.3) + geom_hline(yintercept = -log(0.01, 10),color = 'gray', size = 0.3) + xlim(-5, 5) + ylim(0, 6) + labs(x = 'nLog2 Fold Change', y = 'Log10Mean of Normalized Countn', color = '', title = 'treat vs WTn')#用ggsave输出 ggsave('gene.png', p, width = 5, height = 6) # 标注基因火山图# 这里按p值把显著的上调/下调的前10个基因标出 library(ggrepel) up up down down # 标注无框 p1 geom_text_repel(data = rbind(up, down), aes(x = log2FoldChange, y = -log10(pvalue), label = genename), size = 3,box.padding = unit(0.5, 'lines'), segment.color = 'black', show.legend = FALSE) ggsave ( 'gene1.png', p1, width = 6, height = 6) # 标注有框 p2 geom_label_repel(data = rbind(up, down), aes(label = genename), show.legend = FALSE) ggsave ( 'gene2.png', p2, width = 6, height = 6)