The shape of the graph outputed by REVIGO is broken.

Question

[Riku]

Hi all.

I'm performing GO enrichment analysis in de novo RNAseq analysis.

So, I created a graph with REVIGO and outputed it in R using script exported by REVIGO. But the shape of outputed graph was broken, and the position of value and log_size were reversed.

Why do I get different output even though I use the same script? Is there any way to fix this?

I really appreciated in advance!

Answer 1

[Philipp Bayer]

I've had the same problem recently! I think some publications just screenshot the default output.

The rrvgo package can make a similar plot using the scatterPlot() function: http://www.bioconductor.org/packages/release/bioc/vignettes/rrvgo/inst/doc/rrvgo.html

My own modified R-code based on revigo looks more like this (currently :) ). There are three comments in there where you should customise stuff.

  # data loading here
  library(tidyverse) 
  names(dat) <- c("term_ID","description","frequency", 'plot_X', 'plot_Y', 'log_size', 'value', 'uniqueness', 'dispensability', 'eliminated', 'representative')
  one.data <- dat

  one.data <- one.data [(one.data$plot_X != "null" & one.data$plot_Y != "null") & (! is.na(one.data$frequency)) & (one.data$value != 'null'), ];
  one.data <- type_convert(one.data)

  p1 <-
    ggplot(data = one.data, aes(plot_X, plot_Y, label = description)) +
    geom_point(aes(colour = log(value), size = log_size), alpha = I(0.6)) + # to revert color and size, change the two arguments here
    scale_size_area() +
    scale_colour_gradientn(colours = col_pal, # whatever col_palette you like 
                           limits = c(min(log(one.data$value)), 0)) +
    geom_point(
      aes(plot_X, plot_Y, size = log_size),
      shape = 21,
      fill = "transparent",
      colour = I (alpha ("black", 0.6))
    ) +
    scale_size_area() +
    geom_label_repel(max.overlaps = 5, box.padding = 0.5, # play with max.overlaps to get more or fewer text-boxes
                     aes(point.size = log_size)) +
    theme_minimal() +
    labs(y = "Semantic space x",
         x = "Semantic space y",
         color = 'Log(p-value)',
         size = 'Frequency') +
    theme(
      axis.text.x = element_blank(),
      axis.ticks.x = element_blank(),
      axis.text.y = element_blank(),
      axis.ticks.y = element_blank()
    )
  p1

[Riku]

Sorry for late reply. I'm relieved that you have a solution. I try to use your command before I use screenshots.

Thank you very much for your help!