Code

Single-Cell-Based Clinically-Related Mesoscale Pathology of Pancreatic Cancer

This repository contains all code used to produce the results and figures of the publication "Single-Cell-Based Clinically-Related Mesoscale Pathology of Pancreatic Cancer".

Visulization for figures:

• figure1/figure1.R

  code for plots of heatmap, barplots and tSNE in figure1.

• sup_figure1/sup_fig1.R

  code for boxplots in sfigure2.

• figure2/figure2.R

  code for dotplot, tSNE, circluar barplot and chord plot in figure2.

• figure3/figure3.R

  code for barplots and network graphs in figure3.

• sup_figure3/sup_fig3.R

  code for barplots and network graphs in supplementary figures related to figure3.

• figure4/figure4.R

  code for interaction heatmaps, os analysis and boxplots in figure4.

• sup_figure4/sup_fig4.R

  code for correlation dotplots, density plots, boxplots and os analysis in supplementary figures related to figure4.

• figure5/figure5.R

  code for dotplots, density plot, os analysis and boxplots in figure5.

• image_plot.R for all images of single ROI showed in figures.

  usage example:

  image_plot.R -s p113_normal -t normal
  

• cell_segmentation.cppipe for cell segmentation pipeline of CellProfiler