/single_cell_muti_omics

R code for research paper: A cell-sorting based nano-scale pipeline for cell type-specific multi-omics in plants

Primary LanguageRMIT LicenseMIT

single_cell_muti_omics

R code for data analysis and visualization: A cell-sorting based nano-scale pipeline for cell type-specific multi-omics in plants. DOI:

GO enrichment analysis of proteins enriched in GCP and MCP.

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 analysis of proteomes of DR5 rev::GFP and pOs01g0248900::VENUS-N7 root cells

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.

PCA and Heatmap of metabolomics

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.