r:为什么“断点和标签的长度不同”,如何解决GOplot/chordDiagram?

3ks5zfa0  于 2023-02-14  发布在  Go
关注(0)|答案(1)|浏览(171)

我使用这种方法来生成chord diagrams已经有一段时间了,为了协调我工作中的图形,我需要继续使用这个包。
使用这种方法时,我从未收到过任何错误,而且我也不知道是什么原因导致了这个问题以及如何解决它。
我对“长”数据样本表示歉意,但需要它来重现错误。

问题为什么我会收到此错误,是否可以修复?:

f()中的错误:!分隔符和标签长度不同

library(tidyverse)
library(GOplot)
i_circle <- circle_dat(i_GOterms, i_genelist) %>%
  na.omit() 

chord_i <- chord_dat(data = i_circle, 
                      genes = i_genelist, 
                      process = unique(i_circle$term)) 

GOChord(chord_i)

数据结构1

i_genelist <- structure(list(ID = structure(1:128, levels = c("A1BG", "A2M", 
                                                              "ACTB;ACTG1", "AGT", "AHSG", "ALB", "AMBP", "APLP1", "APOA1", 
                                                              "APOA2", "APOA4", "APOC3", "APOD", "APOE", "APOH", "APP", "AZGP1", 
                                                              "B2M", "B4GAT1", "BCAN", "C1QC", "C1R", "C1S", "C3", "C4A", "C7", 
                                                              "CD14", "CD59", "CDH2", "CFB", "CFH", "CHGA", "CHGB", "CHL1", 
                                                              "CLSTN1", "CLU", "CNDP1", "CNTN1", "CP", "CPE", "CRTAC1", "CSF1", 
                                                              "CSF1R", "CST3", "CTSD", "DAG1", "DKK3", "ECM1", "EFEMP1", "ENPP2", 
                                                              "EPHA4", "EXOC3L4", "F2", "FAM3C", "FBLN1", "FCGBP", "FGA", "FGB", 
                                                              "FGG", "FN1", "FSTL1", "GC", "GM2A", "GRIK1", "HBA1", "HBB", 
                                                              "HP", "HPX", "HSPG2", "IGF2", "IGFBP2", "IGFBP6", "IGFBP7", "IGHA1", 
                                                              "IGHG1", "IGHG2", "IGHG3", "IGKC", "IGLL5;IGLC1", "ITIH2", "ITIH4", 
                                                              "KLK6", "KNG1", "LDHB", "LGALS3BP", "LRG1", "LY6H", "NCAM1", 
                                                              "NCAM2", "NEGR1", "NELL2", "NOV", "NPC2", "NPTXR", "NRCAM", "OGN", 
                                                              "ORM1", "ORM2", "PAM", "PCOLCE", "PCSK1N", "PENK", "PLG", "PLTP", 
                                                              "PSAP", "PTGDS", "RARRES2", "RBP4", "RNASE1", "SCG2", "SCG3", 
                                                              "SCG5", "SERPINA1", "SERPINA3", "SERPINC1", "SERPIND1", "SERPINF1", 
                                                              "SERPING1", "SIRPA;SIRPB1", "SOD3", "SPARCL1", "SPP1", "TF", 
                                                              "TIMP1", "TTR", "VGF", "VSTM2A", "VTN"), class = "factor"), logFC = c(16, 
                                                                                                                                    17, 13, 14, 14, 21, 12, 16, 17, 13, 15, 11, 15, 18, 14, 13, 15, 
                                                                                                                                    16, 13, 14, 12, 13, 11, 18, 17, 11, 13, 14, 14, 14, 15, 15, 14, 
                                                                                                                                    13, 15, 17, 14, 13, 15, 12, 14, 11, 12, 17, 12, 11, 14, 12, 14, 
                                                                                                                                    15, 10, 12, 15, 13, 15, 12, 15, 12, 12, 16, 11, 16, 11, 13, 15, 
                                                                                                                                    16, 17, 17, 10, 12, 12, 11, 14, 14, 18, 14, 16, 16, 13, 12, 11, 
                                                                                                                                    13, 16, 12, 12, 13, 11, 14, 11, 12, 14, 11, 13, 13, 13, 14, 15, 
                                                                                                                                    14, 13, 11, 14, 12, 12, 12, 12, 17, 12, 13, 12, 12, 12, 13, 18, 
                                                                                                                                    15, 13, 11, 16, 15, 14, 12, 16, 12, 19, 11, 16, 15, 12, 14)), row.names = c(NA, 
                                                                                                                                                                                                                -128L), class = "data.frame")

数据结构2

i_GOterms <- structure(list(Category = c("GOTERM_BP_DIRECT", "GOTERM_BP_DIRECT",                         
                                         "GOTERM_BP_DIRECT", "GOTERM_BP_DIRECT", "GOTERM_BP_DIRECT", "GOTERM_BP_DIRECT", 
                                         "GOTERM_BP_DIRECT", "GOTERM_BP_DIRECT", "GOTERM_BP_DIRECT", "GOTERM_BP_DIRECT", 
                                         "GOTERM_BP_DIRECT", "GOTERM_BP_DIRECT", "GOTERM_BP_DIRECT", "GOTERM_BP_DIRECT", 
                                         "GOTERM_BP_DIRECT", "GOTERM_BP_DIRECT", "GOTERM_BP_DIRECT", "GOTERM_BP_DIRECT", 
                                         "GOTERM_BP_DIRECT", "GOTERM_BP_DIRECT"), Term = c("inflammatory response", 
                                                                                           "defense response to bacterium", "plasminogen activation", "positive regulation of B cell activation", 
                                                                                           "phagocytosis, recognition", "high-density lipoprotein particle assembly", 
                                                                                           "negative regulation of fibrinolysis", "negative regulation of blood coagulation", 
                                                                                           "phagocytosis, engulfment", "positive regulation of peptidase activity", 
                                                                                           "protein localization to secretory granule", "protein polymerization", 
                                                                                           "complement activation, alternative pathway", "axon guidance", 
                                                                                           "cholesterol metabolic process", "B cell receptor signaling pathway", 
                                                                                           "negative regulation of very-low-density lipoprotein particle remodeling", 
                                                                                           "regulation of beta-amyloid clearance", "aging", "positive regulation of phagocytosis"
                                         ), Genes = c("SERPINA3, CSF1R, ECM1, ORM1, CSF1, RARRES2, HSPG2, KNG1, C3, C4A, SPP1, CD14, SCG2", 
                                                      "CHGA, IGHG3, IGLL5, IGHG1, IGHG2, VGF, IGKC, HP, IGLC1, IGHA1", 
                                                      "FGB, FGA, APOH, FGG", "IGHG3, IGLL5, IGHG1, IGHG2, IGKC, IGLC1, IGHA1", 
                                                      "IGHG3, IGLL5, IGHG1, IGHG2, IGKC, IGLC1, IGHA1", "APOA2, APOA1, APOA4, APOE", 
                                                      "VTN, APOH, PLG, F2", "VTN, APOH, APOE, KNG1", "IGHG3, IGLL5, IGHG1, IGHG2, IGKC, IGLC1, IGHA1", 
                                                      "APP, FN1, FBLN1, PCOLCE", "CHGA, CPE, SCG3", "FGB, FGA, VTN, FGG", 
                                                      "C3, CFH, C7, CFB", "NELL2, EPHA4, CSF1R, B4GAT1, CHL1, DAG1, CNTN1, NRCAM", 
                                                      "APP, NPC2, APOA2, APOA1, APOA4, APOE", "IGHG3, IGLL5, IGHG1, IGHG2, IGKC, IGLC1, IGHA1", 
                                                      "APOA2, APOC3, APOA1", "APP, APOE, CLU", "SERPINF1, PENK, IGFBP2, DAG1, SERPING1, APOD, TIMP1, AGT", 
                                                      "AHSG, APOA2, SIRPA, APOA1, SIRPB1"), adj_pval = c(0, 0, 0, 0, 
                                                                                                         0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), row.names = c(NA, 
                                                                                                                                                                         -20L), class = "data.frame")
umuewwlo

umuewwlo1#

您需要增加lfc.max,因为您的logFC列中的所有值都超出了默认范围c(-3, 3)

GOChord(chord_i, lfc.max = 20)

我发现这是相当困难的,以适应图例到这个情节,由于长度的术语的标签。

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