python new_prepare_input_df_for_R_GOplot_GOchord.py -g example_data\genes.txt -t example_data\process.txt -er exampl e_data\GO_enrich_result.tsv -ht Term -hg Genes -o output.txt
next we need to use R
df1<-read.csv("output.txt",
header=TRUE,
sep = ",",
row.names = 1,
check.names = FALSE)
df1
df2<-read.csv("example_data/geneslogfc.csv")
df2
identical(rownames(df1),df2$gene_name)
df1$logFC<-df2$logFC
#install.packages("GOplot")
library(GOplot)
library(ggplot2)
p1<-GOChord(as.matrix(df1),
space = 0.02,
gene.order = 'logFC',
gene.space = 0.25,
gene.size = 5)
ggsave(filename = "p3.pdf",
p1,
width = 15,height = 15)
