GOChord plot problem when using the chor_dat function to create a matrix
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2 days ago

Hello All,

I am trying to create a GOChord plot for circular visualization of the results of gene- annotation enrichment analysis. I created all the data frames myself and cross-checked the types of every column in each data frame from the original GitHub page of GOPlot. Everything seems fine. However, when I am trying to run the chor_dat function, I get an error (described below). The data is big so I am unable to share it. I have been struggling to figure out the error and any help will be greatly appreciated.

The code is:

library(GOplot)
library(RColorBrewer)
library(writexl)
library(readxl)
library(ggplot2)
library(gplots)
library(forcats)
library(magrittr)
library(tidyverse)
library(forcats)
library(magrittr)
library(tidyr)
library(dplyr)

Genes_15 <- read_excel("Genes.xlsx")
str(Genes_15)
Genes_15$genes<-as.factor(Genes_15$genes)
str(Genes_15)
Genes_15$logFC <- as.double(Genes_15$logFC)
str(Genes_15)

Circ_data <- read_xlsx("circ.xlsx")
Circ_data_1 <- data.frame(Circ_data)
typeof(Circ_data_1)
str(Circ_data_1)

Process_15 <- read.csv(file = "Process_15_BP.csv")
view(Process_15)
typeof(Process_15)
Process_15_1 <- as.character(Process_15)
str(Process_15_1)

chord <- chord_dat(Circ_data_1, Genes_15, Process_15_1)

The error I am getting is:

Error in as.numeric(levels(genes[, 2]))[genes[, 2]] : invalid subscript type 'list' In addition: Warning message: In if (class(genes[, 2]) != "numeric") genes[, 2] <- as.numeric(levels(genes[, : the condition has length > 1 and only the first element will be used

R GOChord • 40 views
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