Displaying Interactions with chordDiagram in R

Sensitivity analysis is a powerful tool to find out which parameters in a model have the largest effect on the results. Besides the impact of the main parameters, exploring the interactions between parameters is also important because complex systems usually have many active interactions. Learning from them will improve our understanding of how a model works at different underlying conditions. This could potentially lead to improving our inferences of the model’s results and model evaluation. Previously, Antonio showed how to create a Radial convergence plot for visualizing Sobol indices in Python. In this blog post, I am going to use a library in R to create a Chord diagram for Sobol interaction indices for annual baseflow. Then, I will create an animated GIF file that shows the interactions for a few years. The dataset (download from here) that I am using came from the simulation of an agro-biophysical model that has 33 parameters.

install.packages("circlize")
library(circlize)
baseflow_S2<- read.csv(paste("...(your path).../sobol_ Baseflow_S2_1989.csv",sep=""))
baseflow_S2$X<- NULL

To work with this library, the format of the data should be a matrix or list.

baseflow_S2<- as.matrix(baseflow_S2)

As I mentioned above, the interactions are between 33 parameters, so we have 33 rows and columns in this dataset. I am going to assign a name to each row and column based on the actual order in the dataset:

rownames(baseflow_S2) = c("H_1","H_2","H_3","H_4","B_1","B_2","B_3","B_4","B_5","W_4","W_5","T_4","W_1","W_2","W_6","W_7","Phy_1","Phy_2","T_1","T_2","W_3","Phy_3","Phy_4","T_3","Phy_5","Phy_6","H_5","Ph_1","Ph_2","Ph_3","Ph_4","Ph_5","Ph_6")                   
colnames(baseflow_S2)= c("H_1","H_2","H_3","H_4","B_1","B_2","B_3","B_4","B_5","W_4","W_5","T_4","W_1","W_2","W_6","W_7","Phy_1","Phy_2","T_1","T_2","W_3","Phy_3","Phy_4","T_3","Phy_5","Phy_6","H_5","Ph_1","Ph_2","Ph_3","Ph_4","Ph_5","Ph_6") 	       

Now, we are going to assign a color for each parameter. For better visualization and interpretability of the results, these parameters are classified into six main groups (H, Ph, B, T, W, and Phy) based on how they are related to the model. I am going to assign the same color to all of the parameters within each group.

grid.col=c(H_1="deepskyblue4",H_2="deepskyblue4",H_3="deepskyblue4",H_4="deepskyblue4",H_5="deepskyblue4",Ph_1="darkorange3",Ph_2="darkorange3",Ph_3="darkorange3",Ph_4="darkorange3",Ph_5="darkorange3",Ph_6="darkorange3",B_1="brown4",B_2="brown4",B_3="brown4",B_4="brown4",B_5="brown4",T_1="coral2",T_2="coral2",T_3="coral2",T_4="coral2",W_1="cyan3",W_2="cyan3",W_3="cyan3",W_4="cyan3",W_5="cyan3",W_6="cyan3",W_7="cyan3",Phy_1="darkgreen",Phy_2="darkgreen",Phy_3="darkgreen",Phy_4="darkgreen",Phy_5="darkgreen",Phy_6="darkgreen")

Now we can look at the plot:

interactions_plot<- chordDiagram(baseflow_S2,grid.col = grid.col )

As we see, there are many small interactions between parameters. Therefore, you may want to set a limit to show some specific interactions that are large, or you may just want to clean up some of the interactions that are less than specific values. To do this task, we can use the result of the above function without any more adjustments in order to get the final format of a dataset that is created within the function. Then, we can modify it based on what we want to show. The “interactions_plot” is actually a plot, but you can also look at its data frame. The “col” column has the color code that is assigned to each interaction. We can extract that column.

 col2<- interactions_plot$col

Then get the index of values that are less than for example 0.005:

idx <- which(interactions_plot$value2 < 0.005, arr.ind = TRUE)

And we can replace the actual color in “col2” with “transparent” for those rows for which their index was selected above.

col2[idx] <- 'transparent'

Now, we can create a final graph with some more adjustments: with “order,” we can manually sort a grid (sectors). “link.sort” and “link.decreasing” are used to sort the links based on the value of the interaction (which is shown by the width of the sector). This might help in detecting interesting interactions: “annotationTrack” set to “grid”, print the sectors, “preAllocateTracks”, specified the track, “circos.track” creates plotting regions for a track: track.index is the index for the track, which is going to be updated. “panel.fun” is used to add graphics and customize sector labels (x and y correspond to the data points in each cell).

chordDiagram(baseflow_S2,order = c("H_1","H_2","H_3","H_4","H_5","Ph_1","Ph_2","Ph_3","Ph_4","Ph_5","Ph_6","B_1","B_2","B_3","B_4","B_5","T_1","T_2","T_3","T_4","W_1","W_2","W_3","W_4","W_5","W_6","W_7","Phy_1","Phy_2","Phy_3","Phy_4","Phy_5","Phy_6"),grid.col = grid.col ,col=col2, link.sort = TRUE, link.decreasing = TRUE,annotationTrack = "grid", preAllocateTracks = list(1))
title(main=paste(1989),adj=0)
    circos.track (track.index = 1, panel.fun = function(x, y) {
      xlim = get.cell.meta.data("xlim")
      ylim = get.cell.meta.data("ylim")
      sector.name = get.cell.meta.data("sector.index")
      circos.text(mean(xlim), ylim[1]+.1, sector.name, facing = "clockwise", niceFacing = TRUE, adj = c(-0.5,0.5),cex = 0.6)
      circos.axis(h = "top", labels.cex = 0.6, major.tick.percentage = 0.2, track.index = 2)}, bg.border = NA) 

We may want to add another layer to highlight a specific sector and add a group name. In this case, we can use “highlight.sector” to specify the color, label, and components of this new layer. With “padding,” we can also change the width of this layer.

highlight.sector(rownames(baseflow_S2[c("H_1","H_2","H_3","H_4","H_5"),]), track.index = 1, col = "deepskyblue4",text = "H", cex = 0.8, text.col = "black", niceFacing = TRUE,padding = c(-0.9, 0, 0.27, 0),font=2) 

highlight.sector(rownames(baseflow_S2[c("Ph_1","Ph_2","Ph_3","Ph_4","Ph_5","Ph_6"),]), track.index = 1, col = "darkorange3", text = "PH", cex = 0.8, text.col = "black", niceFacing = TRUE,padding = c(-0.9, 0, 0.27, 0),font=2)

highlight.sector(rownames(baseflow_S2[c("T_1","T_2","T_3","T_4"),]), track.index = 1, col = "coral2", text = "T", cex = 0.8, text.col = "black", niceFacing = TRUE,padding = c(-0.9, 0, 0.27, 0),font=2)   

highlight.sector(rownames(baseflow_S2[c("Phy_1","Phy_2","Phy_3","Phy_4","Phy_5","Phy_6"),]), track.index = 1, col = "darkgreen",text = "PHY", cex = 0.8, text.col = "black", niceFacing = TRUE,padding = c(-0.9, 0, 0.27, 0),font=2)

highlight.sector(rownames(baseflow_S2[c("B_1","B_2","B_3","B_4","B_5"),]), track.index = 1, col = "brown4", text = "B", cex = 0.8, text.col = "black", niceFacing = TRUE,padding =c(-0.9, 0, 0.27, 0),font=2) 

highlight.sector(rownames(baseflow_S2[c("W_1","W_2","W_3",	"W_4","W_5","W_6","W_7"),]), track.index = 1, col = "cyan3",text = "W", cex = 0.8, text.col = "black", niceFacing = TRUE,padding = c(-0.9, 0, 0.27, 0),font=2)

And here is the final plot:

To save the graph use this line of code before calling the chordDiagram():

png(file = paste("…(your path)…./sobol_Baseflow_S2_1989.png",sep="") ,height = 7, width = 7, units = "in", res = 500) 

And at the end run dev.off(). Now, I am going to run this code for all of the other years and save them to make a GIF file that shows the interactions for all years. To make an animation from these plots, first we need to install “magick package.”

This simple code reads the first image and then adds the rest of the images to that in a loop. You can also add a message for each image. (Here, I added the year.) The “delay” option is used to adjust the delay after each frame.   

install.packages("magick")
library(magick)
img <- image_read(path = paste0("...(your path).../sobol_Baseflow_S2_1989.png"))
years<- as.data.frame(1989:1997)

for(Y in 1:nrow(years)) {
img0 <- image_read(path = paste0("...(your path).../sobol_Baseflow_S2_",years[Y,],".png"))
img <- c(img, img0) 
}  
img1 <- image_scale(image = img, geometry = "720x720")
ani0 <- image_animate(image = img1, delay = 200)
image_write(image = ani0, path = paste0("...(your path).../sobol_Baseflow_S2.gif"))

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