How to merge figures into one graph

How to merge figures into one graph

In ViewBS, all the figure objects will be saved into RDS files. The users can restore the RDS files and merge the figures into one graph.

There are two ways to do this: 1) use the helper script named mer_fig.R ; 2) the users can write R script to read the RDS files and merge the figures into one graph with cowplot.

1. Use the R script in ViewBS to do so:

Example as below:

cd $PATH2testdata
Rscript ../../lib/scripts/mer_fig.R --input BisNonConvRate/cmt2_proj_allsam.tab.rds,MethGlobal/cmt2_proj_allsam.tab.rds,MethHeatmap/CHG_hypo_DMR_drm12cmt23_to_WT_MethHeatmap_CHG.pdf.rds --output testplot_col2.pdf --aspect_ratio 1.5 --ncol 2

Please see the following for the help information:

$ Rscript ../../lib/scripts/mer_fig.R -h

USAGE
    Usage: Rscript mer_fig.R --input <fig1.rds,fig2.rds> --labels <A,B,C,D> [options]

DESCRIPTION
    mer_fig.R is developed to merge figures into on graph.

Options
    -help | -h
            Prints the help message and exits.

    --input [required]
           - RDS files. <fig1.rds,fig2.rds...>

    --labels [optional]
           - Labesl for each figure. Default: <A,B,C,D...>

    --output [optional]
           - Output files for the graph. Default: cowplot_mer_fig.pdf

    --ncol [optional]
           - Number of columns on the graph.

    --base_height [optional]
           - The height (in inches) of each sub-plot

    --base_aspect_ratio [optional]
           -  The aspect ratio of each sub-plot. Default: 1.6

Error: Please check the help information!
Execution halted

2. Use the template below to merge multiple figures into one graph.

library(cowplot) # https://cran.r-project.org/web/packages/cowplot/vignettes/introduction.html
p1 <- readRDS("BisNonConvRate/cmt2_proj_allsam.tab.rds")
p2 <- readRDS("MethGlobal/cmt2_proj_allsam.tab.rds")

plot2by2 <- plot_grid(p1, p2,
                      labels=c("A", "B"), ncol = 2)

save_plot("plot2by2.pdf", plot2by2,
          ncol = 2, # we're saving a grid plot of 2 columns
          #nrow = 2, # and 2 rows
          # each individual subplot should have an aspect ratio of 1.3
          base_aspect_ratio = 2
          )

Here is how plot2by2.png looks like:

Further improvement of the graph can be done in Inkscape if a PDF file was generated.