Customized Circle packing with R and ggraph - error saying the data frame should contain at least two columns - Stack Overflow

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I am trying to create a circle packing figure, and keep getting the following error message:

"Error in graph_from_data_frame(edges, vertices = vertices) : 
 the data frame should contain at least two columns"

I am trying to create a circles for the HPV variants that exist in HPVseq_p and then subcircles for those that exist in HPVseq_s. (ie a big circle for HPV16 that then contains the various HPV variants inside it for HPVseq_s (HPV16, HPV53)

my code is below:

library(ggraph)
library(igraph)
library(tidyverse)
library(viridis)    
edges <- HPV_subtypes$HPVseq_p
vertices <- HPV_subtypes$HPVseq_s
mygraph <- graph_from_data_frame(edges, vertices=vertices)`

dput(mydata_compressed)
structure(list(Sample = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10), HPVseq_p = c("HPV16", 
"HPV16", "HPV16", "HPV16", "HPV16", "HPV16", "HPV16", "HPV16", 
"HPV16", "HPV33"), HPVseq_s = c("HPV16", "HPV53", "HPV16", "HPV16", 
"HPV16", "HPV16", "HPV16", "HPV16", "HPV16", "na"), HPVdPCR_p = c("HPV16", 
"HPV16", "na", "HPV16", "HPV16", "HPV16", "HPV16", "HPV16", "HPV16", 
"HPV33"), HPVdPCR_s = c("HPV16", "HPV16", "HPV16", "HPV16", "HPV16", 
"HPV16", "HPV16", "na", "HPV16", "na")), row.names = c(NA, -10L
), class = c("tbl_df", "tbl", "data.frame"))

im new at this, help would be appreciated!

I am trying to create a circle packing figure, and keep getting the following error message:

"Error in graph_from_data_frame(edges, vertices = vertices) : 
 the data frame should contain at least two columns"

I am trying to create a circles for the HPV variants that exist in HPVseq_p and then subcircles for those that exist in HPVseq_s. (ie a big circle for HPV16 that then contains the various HPV variants inside it for HPVseq_s (HPV16, HPV53)

my code is below:

library(ggraph)
library(igraph)
library(tidyverse)
library(viridis)    
edges <- HPV_subtypes$HPVseq_p
vertices <- HPV_subtypes$HPVseq_s
mygraph <- graph_from_data_frame(edges, vertices=vertices)`

dput(mydata_compressed)
structure(list(Sample = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10), HPVseq_p = c("HPV16", 
"HPV16", "HPV16", "HPV16", "HPV16", "HPV16", "HPV16", "HPV16", 
"HPV16", "HPV33"), HPVseq_s = c("HPV16", "HPV53", "HPV16", "HPV16", 
"HPV16", "HPV16", "HPV16", "HPV16", "HPV16", "na"), HPVdPCR_p = c("HPV16", 
"HPV16", "na", "HPV16", "HPV16", "HPV16", "HPV16", "HPV16", "HPV16", 
"HPV33"), HPVdPCR_s = c("HPV16", "HPV16", "HPV16", "HPV16", "HPV16", 
"HPV16", "HPV16", "na", "HPV16", "na")), row.names = c(NA, -10L
), class = c("tbl_df", "tbl", "data.frame"))

im new at this, help would be appreciated!

• r
• ggraph
• circle-pack

Share Improve this question Follow asked Mar 14 at 6:30 peaches523peaches523 122 bronze badges

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1 Answer 1

Sorted by: Reset to default 0

I don´t know what is contained in your HPV_subtypes object, but if it is the tibble that can be created from the code below, then you´re passing a vector to the d argument in graph_from_data_frame . Instead you need to pass a dataframe with two columns (the first two in your dataframe), usually named from and to, which specify the association between your components in the dataframe. The remaining columns are regarded as edge attributes, if the vertices argument is NULL , which is the default. Have a look at the example from the ?graph_from_data_frame help page.

What do you want to achieve with this code? is it just for visualization, or do you want to use this graph for computation purposes?

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