'sig']='up'difexp.loc[(difexp.fold<-1)&(difexp.pvalue<0.05),'sig']='down'difexp['log(pvalue)']=-np.log10(difexp['pvalue'])ax=sns.scatterplot(x="fold",y="log(pvalue)",hue='sig
colnames(datTraits))# 获取模块内的基因moduleGenes = moduleColors == modulesizeGrWindow(7, 7);par(mfrow = c(1,1));verboseScatterplot(abs(geneModuleMembership[moduleGenes,module_column]),abs(geneTraitSignificance[moduleGenes, 1]),xlab = paste("Module Membership in", module, "...
sizeGrWindow(7, 7);par(mfrow = c(1,1));verboseScatterplot(abs(geneModuleMembership[moduleGenes,module_column]),abs(geneTraitSignificance[moduleGenes, 1]),xlab = paste("Module Membership in", module,"module"),ylab = paste("Gene significance for", pheno),main = paste("Module membership vs...
https://www.omicshare.com/tools/home/report/report_diff_scatter_chart.html 在多组差异火山图中,以组间差异倍数的对数值log2FC为纵坐标,以比较组的名称为横坐标,可完美地在一张图中一次性展示多个比较组的差异基因: OmicShare动态多组差异散点图绘制示例 ...
Scatter plots denote the level of artifactual TSO-UMI reads and RNA counting errors (l) as well as a percentage of ribosomal RNA (rRNA) mapped reads and number of detected genes in 100,000 reads after removal of strand invasion reads (m). n, Benchmarking of Smart-seq3 variants. Box ...
WGCNA (weighted gene co-expression network analysis)权重基因共表达网络分析(流程模块见下图),可将表达模式相似的基因进行聚类,并分析模块与特定性状或表型之间的关联,常用于筛选关键表型的hub基因 ,是RNAseq分析中的一块很重要的拼图。而之所以叫组学数据黏合剂
C: Intensity Scatter Plot (密度分散图) D: Heatmap (热图) E: Gene Ontology (GO) analysis F: GO analysis 如果你认真看完本篇文章,你也能够做出从A到F这些图。 结合之前文章提到的配色方案(关于配色问题,参考以下链接),你会做出很漂亮的A-F,然后开心地放在PPT和论文中!
(deg.data$FDR) # 绘制基本热图 ggscatter(deg.data, x = "log2FC", y = "logQ") + theme_base() # 新加一列Group deg.data$Group = "normal" # 将adj.P.Val小于0.05,logFC大于2 # 将adj.P.Val小于0.05,logFC小于2的基因设为显著下调基因 deg.data$Group[which( (deg.data$FDR < 0.01) ...
WGCNA的标配热图TOMplot / Network heapmap plot,描绘了分析中所有基因之间的拓扑重叠矩阵(TOM),颜色越深表示基因之间的相关性越大; Eigengene-adjacency-heatmap 展示基因模块之间的相关性,还可以加入表型信息,查看表型与哪些模块相关性高 ### 5. WGCNA可视化:TOMplot Eigengene-adjacency-heatmap ### rm(list = ...
Scatter plot of SL RNA-Seq data comparing mRNA abundance between purine-replete and purine-starved cells.Jessica, L. MartinPhillip, A. YatesRadika, SoysaJoshua F., AlfaroFeng, YangKristin, E. BurnumJohnsonVladislav A., PetyukKarl K., Weitz...