Error during wrapup: subscript out of bounds

[FarzanehRah]

Hello, when I use : (p2 <- ggNestedBarChart(p)) I get this error: Error during wrapup: subscript out of bounds Error: no more error handlers available (recursive errors?); invoking 'abort' restart. Any solution? Thank you

[davedgd]

I haven't seen that one before and am not getting that error message with the example code.

Do you have some data and associated script you could provide for context so I can debug further?

[FarzanehRah]

Thank you so much for your rapid reply!

data <- read.csv("data.txt", sep ="\t", header = TRUE, stringsAsFactors = FALSE)

data $category_f = factor(data$category, levels=c('regulation','overallProfile_iRNA_Variety','overallProfile_MIR_Variety','overallProfile_SIR_Variety'))
data$Variety_f = factor(data$Variety, levels=c("-", "Manitou", "IsoS8", "Norstar", "IsoW11"))

p <- ggplot(data, aes(x= Clusters, y=TermsDesc, size=Count, color=Pvalue, group=Clusters)) + geom_point(alpha = 0.8) +  theme_bw(base_size = 14) + ylab(NULL) + xlab(NULL) +

  scale_color_gradient(low =  "seagreen",  high = "red", space = "Lab", limit = c(0.0, 0.06)) + scale_size(range =  c(1,7), breaks = c(2,20,40,60,80,100,119)) +
  theme(legend.key=element_blank(), 
        axis.text.x = element_text(colour = "black", size = 9, angle = 90, vjust = 0.3, hjust = 1, face = "bold"), 
        axis.text.y = element_text(colour = "black", size = 12, face = "bold"), 
        legend.text = element_text(size = 10, colour ="black"), 
        legend.title = element_text(size = 11), panel.background = element_blank(), 
        panel.border = element_rect(colour = "black", fill = NA, size = 1), 
        legend.position = "right", panel.grid.major.y = element_line(colour = "grey"))+
  facet_grid(enrichment ~ category_f + Variety_f, scales = "free", space = "free",)+ 
  theme(strip.text.y = element_text(size = 10, angle = 45,face = "bold")) + theme(strip.text.x  = element_text(size = 10,angle = 90, face = "bold")) + labs(title="Enrichment analysis") + theme(plot.title = element_text(face="bold", size=14)) 

(p2 <- ggNestedBarChart(p))

[FarzanehRah]

data.txt

[davedgd]

You're welcome, and this is helpful!

I took a look at the example, and the main issue is this package is only designed to work with bar plots that look more like p1 in the example using facet_wrap.

By comparison the plot for p based on the code you provided involves points, uses facet_grid, and seems to use a two-level grouping variable (i.e., grouping on both the x- and y-axis of the plot, which is another feature ggNestedBarPlot wasn't designed to do).

I played around with the code briefly to see if there is a way to adapt it to your p plot, but unfortunately the underlying logic in the ggNestedBarChart function would require a complete rewrite to make it work with this input, and I'm ultimately not entirely clear on what the output ought to look like either.

Sorry this isn't more helpful!

[FarzanehRah]

Thank you so much for your explanation!

[davedgd]

You're welcome! If I have ever have time to come back to this package to flesh it out, I'll try to cover more potential use cases. Thanks again for reaching out with questions!