Pie Charts in RCy3

random-code-snippets rcy3 cyoscape R

How to represent nodes as pie charts using Cytoscape and RCy3

Robert M Flight true
2022-01-06

I have a package, categoryCompare2 (Flight 2022) that I’ve been working on for a while, and recently wanted to make available on our labs r-universe (“The ’Moseleybioinformaticslab’ Universe,” n.d.).

For some of the current visualization, we use Cytoscape to examine annotation similarity graphs, coupling the R together with Cytoscape via RCy3 (Gustavsen et al. 2019). In the previous iteration, we had used actual piechart images generated by R, and then used {setNodeImageDirect} to point the node images to local image files.

However, the latest iteration of RCy3 has essentially lost that functionality. However, there is a new visualization plugin that can do similar things, enhancedGraphics (Morris JH 2014).

Alexander Pico, one of the primary RCy3 developers, provided me with the guidance for a code solution (Pico 2022), which I’ve adapted below.

grp_matrix = matrix(c(1, 0,
                      0, 1), nrow = 2, ncol = 2)
n_grp <- nrow(grp_matrix)
use_color <- rainbow_hcl(ncol(grp_matrix), c = 100)
n_color <- length(use_color)
use_color = color
# defines how many pie segments are needed, common to all the pie-charts
pie_area <- rep(1 / n_color, n_color)
names(pie_area) <- rep("", n_color)


desat_color <- desaturate(use_color)
names(desat_color) <- names(use_color)
piechart_strings <- purrr::map_dfr(rownames(grp_matrix), function(i_grp){
  tmp_logical <- grp_matrix[i_grp, ]
  tmp_color <- use_color
    
  # add the proper desaturated versions of the colors
  tmp_color[!tmp_logical] <- desat_color[!tmp_logical]
    
  out_str = paste0('piechart: attributelist="',
                   paste(colnames(grp_matrix), collapse = ','),
                   '" ',
                   'colorlist="',
                   paste(tmp_color, collapse = ','),
                   '" ',
                   'arcstart=-90 showlabels=false')
  data.frame(colorlist = out_str)
})

tmp_matrix = as.data.frame(matrix(1, nrow = nrow(piechart_strings),
                      ncol = ncol(grp_matrix)))
names(tmp_matrix) = colnames(grp_matrix) 
piechart_df = cbind(tmp_matrix, piechart_strings)

# after merging this with the node information to
# put the right things with the right node
# this gives **node_vis_df** below
RCy3::setNodeShapeDefault("ELLIPSE")
RCy3::setNodeSizeDefault(35)
RCy3::loadTableData(node_vis_df, data.key.column = "name", table = "node", table.key.column = "name")
RCy3::updateStyleMapping("default",
   RCy3::mapVisualProperty("NODE_CUSTOMGRAPHICS_1", "colorlist", "p"))
Flight, Robert M. 2022. “categoryCompare2.” https://github.com/MoseleyBioinformaticsLab/categoryCompare2.
Gustavsen, Julia A., Pai, Shraddha, Isserlin, Ruth, Demchak, Barry, Pico, and Alexander R. 2019. “RCy3: Network Biology Using Cytoscape from Within r.” F1000Research. https://doi.org/10.12688/f1000research.20887.3.
Morris JH, Ferrin TE, Kuchinsky A. 2014. “enhancedGraphics: A Cytoscape App for Enhanced Node Graphics.” F1000Research. https://doi.org/10.12688/f1000research.4460.1.
Pico, Alexander. 2022. “RCy3 GitHub Issue: Equivalent of setNodeImageDirect.” https://github.com/cytoscape/RCy3/issues/167#issuecomment-1004467137.
“The ’Moseleybioinformaticslab’ Universe.” n.d. https://moseleybioinformaticslab.r-universe.dev/ui#builds.

References

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Text and figures are licensed under Creative Commons Attribution CC BY 4.0. Source code is available at https://github.com/rmflight/researchBlog_distill, unless otherwise noted. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".

Citation

For attribution, please cite this work as

Flight (2022, Jan. 6). Deciphering Life: One Bit at a Time: Pie Charts in RCy3. Retrieved from https://rmflight.github.io/posts/2022-01-06-pie-charts-in-rcy3/

BibTeX citation

@misc{flight2022pie,
  author = {Flight, Robert M},
  title = {Deciphering Life: One Bit at a Time: Pie Charts in RCy3},
  url = {https://rmflight.github.io/posts/2022-01-06-pie-charts-in-rcy3/},
  year = {2022}
}