R code for data analysis and visualization: A cell-sorting based nano-scale pipeline for cell type-specific multi-omics in plants. DOI:
The GO enrichment analysis and visualize of GCP and MCP was performed by ClusterProfiler V4.0.2. R package org.At.tair.db v 3.14 were used as the orgDb of Arabidopsis thaliana.
The GO enrichment analysis was performed by agrigo. For DR5 rev::GFP the arabidopsis thaliana TAIR10 GO annotation was used as the GO background. For pOs01g0248900::VENUS-N7 the Oryza sativa subsp. japonica (Rice) GO annotation was used as the GO background. The GO term redundancy was removed by REViGO, besides, a GO term network was generated by REViGO. The .xgmml file were convert into .graphml by cytoscape v3.9.0. And the final network were generated by gephi v0.92.
Raw peak area was used as the input data of PCA. and R package PCAtools were used as the PCA analysis and visualize. ComplexHeatmap was used to generate the heatmap.