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Enter the body of text here I am trying to make a cnetplot for my data. Input is an enrichResult obj. I am following the instructions for Cnetplot for rnrichResult obj given in the manual of enrichplot package but still getting this error. Can someone please help me with that? Code should be placed in three backticks as shown below
# include your problematic code here with any corresponding output
library(clusterProfiler)
library(org.Mm.eg.db)
library(biomaRt)
library(GOSemSim)
library(readr)
library(enrichplot)
library(DOSE)
cnetplot(
+ enrichment,
+ layout = igraph::layout_with_kk,
+ showCategory = 5,
+ color_category = "#E5C494",
+ size_category = 1,
+ color_item = "#B3B3B3",
+ size_item = 1,
+ color_edge = "grey",
+ size_edge = 0.5,
+ node_label = "all",
+ foldChange = NULL,
+ hilight_alpha = 0.3,
+ )
sessionInfo( )
Error in graph_from_data_frame(d = d, directed = directed, vertices = vertices) :
the data frame should contain at least two columns
In addition: Warning messages:
1: In cnetplot.enrichResult(x, ...) :
Use 'color.params = list(foldChange = your_value)' instead of 'foldChange'.
The foldChange parameter will be removed in the next version.
2: In cnetplot.enrichResult(x, ...) :
Use 'color.params = list(edge = your_value)' instead of 'colorEdge'.
The colorEdge parameter will be removed in the next version.
3: In cnetplot.enrichResult(x, ...) :
Use 'color.params = list(category = your_value)' instead of 'color_category'.
The color_category parameter will be removed in the next version.
# please also include the results of running the following in an R session