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Published 20 hours ago • verified publisher icon jokergoo

chordDiagram fail to recongize all section

Open mliu86 opened this issue 6 months ago • 0 comments

data_long

A tibble: 136 × 7

Ligand To_Receptors Value LigandColor ReceptorColor ConnectionColor Short_Receptors
1 HSPG2 Vascular cells_DAG1 0.700 #F8766D #00B8E7 #FF0000FF DAG1
2 INS1 Vascular cells_INSSR 0.156 #F8766D #00B8E7 #FFD4C6FF INSSR
3 INS2 Vascular cells_INSSR -0.338 #F8766D #00B8E7 #F7F0FFFF INSSR
4 JAM2 Vascular cells_JAM3 -5.41 #F8766D #00B8E7 #0000FFFF JAM3
5 JAM2 Vascular cells_F11R -5.41 #F8766D #00B8E7 #0000FFFF F11R
6 JAM3 Vascular cells_F11R 0.210 #F8766D #00B8E7 #FFC5B2FF F11R
7 SFTPD Vascular cells_ADGRE5 0.700 #F8766D #00B8E7 #FF0000FF ADGRE5
8 SPP1 Vascular cells_ITGA9_ITGB1 -5.41 #F8766D #00B8E7 #0000FFFF ITGB1
9 SPP1 Vascular cells_ITGA5_ITGB1 -5.41 #F8766D #00B8E7 #0000FFFF ITGB1
10 TENM4 Vascular cells_ADGRL2 0.700 #F8766D #00B8E7 #FF0000FF ADGRL2

chordDiagram(data_long, grid.col = colors, col = data_long$ConnectionColor, directional = T,

  •          annotationTrack = "grid", big.gap = 10, small.gap = 0,

  •          preAllocateTracks = list(track.height = 0.1), link.target.prop = F, 

  •          transparency = 0.5)

get.all.sector.index() [1] "HSPG2" "INS1" "INS2"
[4] "JAM2" "JAM3" "SFTPD"
[7] "SPP1" "TENM4" "WNT4"
[10] "FLRT1" "NRXN1" "TENM2"
[13] "TENM3" "UNC5A" "PPY"
[16] "PYY" "APP" "GCG"
[19] "ITGAV" "Vascular cells_DAG1" "Vascular cells_INSSR"
[22] "Vascular cells_JAM3" "Vascular cells_F11R" "Vascular cells_ADGRE5"
[25] "Vascular cells_ITGA9_ITGB1" "Vascular cells_ITGA5_ITGB1" "Vascular cells_ADGRL2"
[28] "Vascular cells_FZD4_LRP5" "Gamma_ADGRL3" "Gamma_DAG1"
[31] "Gamma_ITGAV_ITGB1" "Gamma_JAM3" "Gamma_F11R"
[34] "Gamma_CLSTN1" "Gamma_FLRT1_ADGRL3" "Gamma_ADGRL1"
[37] "Gamma_FLRT1_ADGRL1" "Gamma_FZD3_LRP6" "Stellate 2_DAG1"
[40] "Stellate 2_ITGAV_ITGB1" "Stellate 2_JAM3" "Stellate 2_F11R"
[43] "Stellate 2_CLSTN1" "Stellate 2_NPY1R" "Stellate 2_ADGRE5"
[46] "Stellate 2_CD44" "Stellate 2_ITGAV_ITGB3" "Stellate 2_ITGAV_ITGB5"
[49] "Stellate 2_ITGA9_ITGB1" "Stellate 2_ITGA5_ITGB1" "Stellate 2_ADGRL1"
[52] "Stellate 2_FLRT1_ADGRL1" "Stellate 2_ADGRL2" "Stellate 1_TNFRSF21"
[55] "Stellate 1_DAG1" "Stellate 1_ITGAV_ITGB1" "Stellate 1_JAM3"
[58] "Stellate 1_NPY1R" "Stellate 1_ADGRE5" "Stellate 1_ITGAV_ITGB5"
[61] "Delta 2_INSSR" "Delta 2_ADGRL1" "Delta 2_CD44"
[64] "Delta 2_FLRT1_ADGRL1" "Delta 2_FZD3_LRP6" "Delta 1_SORL1"
[67] "Delta 1_DAG1" "Delta 1_INSSR" "Delta 1_JAM3"
[70] "Delta 1_F11R" "Delta 1_ADGRL1" "Delta 1_CLSTN3"
[73] "Delta 1_CD44" "Delta 1_FLRT1_ADGRL1" "Delta 1_ADGRL2"
[76] "Delta 1_FZD3_LRP6" "Alpha 2_ADGRL1" "Alpha 2_FLRT1_ADGRL1"
[79] "Alpha 1_ADGRL1" "Alpha 1_DAG1" "Alpha 1_INSSR"
[82] "Alpha 1_ITGAV_ITGB1" "Alpha 1_JAM3" "Alpha 1_F11R"
[85] "Alpha 1_NLGN2" "Alpha 1_CLSTN3" "Alpha 1_FLRT1_ADGRL1"
[88] "Alpha 1_FZD3_LRP6" "Beta 2_GIPR" "Beta 2_ADGRL1"
[91] "Beta 2_FLRT1_ADGRL1" "Beta 1_SORL1" "Beta 1_ADGRL1"
[94] "Beta 1_DAG1" "Beta 1_INSSR" "Beta 1_ITGAV_ITGB1"
[97] "Beta 1_JAM3" "Beta 1_F11R" "Beta 1_NLGN2"
[100] "Beta 1_CLSTN1" "Beta 1_CLSTN3" "Beta 1_CD44"
[103] "Beta 1_ITGAV_ITGB5" "Beta 1_FLRT1_ADGRL1" "Beta 1_FZD3_LRP6"
[106] "Proliferating cells_SORL1" "Proliferating cells_ITGB1_ADGRE5" "Proliferating cells_ITGAV_ITGB1" [109] "Proliferating cells_F11R" "Proliferating cells_ADGRE5" "Proliferating cells_CD44"
[112] "Proliferating cells_ITGAV_ITGB5" "Proliferating cells_ADGRL1" "Proliferating cells_FLRT1_ADGRL1" [115] "Proliferating cells_FZD3_LRP6"

unique(c(data_long$Ligand,data_long$To_Receptors)) [1] "HSPG2" "INS1" "INS2"
[4] "JAM2" "JAM3" "SFTPD"
[7] "SPP1" "TENM4" "WNT4"
[10] "FLRT1" "NRXN1" "TENM2"
[13] "TENM3" "UNC5A" "PPY"
[16] "PYY" "APP" "GCG"
[19] "ITGAV" "Vascular cells_DAG1" "Vascular cells_INSSR"
[22] "Vascular cells_JAM3" "Vascular cells_F11R" "Vascular cells_ADGRE5"
[25] "Vascular cells_ITGA9_ITGB1" "Vascular cells_ITGA5_ITGB1" "Vascular cells_ADGRL2"
[28] "Vascular cells_FZD4_LRP5" "Gamma_ADGRL3" "Gamma_DAG1"
[31] "Gamma_ITGAV_ITGB1" "Gamma_JAM3" "Gamma_F11R"
[34] "Gamma_CLSTN1" "Gamma_FLRT1_ADGRL3" "Gamma_ADGRL1"
[37] "Gamma_FLRT1_ADGRL1" "Gamma_FZD3_LRP6" "Stellate 2_DAG1"
[40] "Stellate 2_ITGAV_ITGB1" "Stellate 2_JAM3" "Stellate 2_F11R"
[43] "Stellate 2_CLSTN1" "Stellate 2_NPY1R" "Stellate 2_ADGRE5"
[46] "Stellate 2_CD44" "Stellate 2_ITGAV_ITGB3" "Stellate 2_ITGAV_ITGB5"
[49] "Stellate 2_ITGA9_ITGB1" "Stellate 2_ITGA5_ITGB1" "Stellate 2_ADGRL1"
[52] "Stellate 2_FLRT1_ADGRL1" "Stellate 2_ADGRL2" "Stellate 1_TNFRSF21"
[55] "Stellate 1_DAG1" "Stellate 1_ITGAV_ITGB1" "Stellate 1_JAM3"
[58] "Stellate 1_NPY1R" "Stellate 1_ADGRE5" "Stellate 1_ITGAV_ITGB5"
[61] "Delta 2_INSSR" "Delta 2_ADGRL1" "Delta 2_CD44"
[64] "Delta 2_FLRT1_ADGRL1" "Delta 2_FZD3_LRP6" "Delta 1_SORL1"
[67] "Delta 1_DAG1" "Delta 1_INSSR" "Delta 1_JAM3"
[70] "Delta 1_F11R" "Delta 1_ADGRL1" "Delta 1_CLSTN3"
[73] "Delta 1_CD44" "Delta 1_FLRT1_ADGRL1" "Delta 1_ADGRL2"
[76] "Delta 1_FZD3_LRP6" "Alpha 2_ADGRL1" "Alpha 2_FLRT1_ADGRL1"
[79] "Alpha 1_ADGRL1" "Alpha 1_DAG1" "Alpha 1_INSSR"
[82] "Alpha 1_ITGAV_ITGB1" "Alpha 1_JAM3" "Alpha 1_F11R"
[85] "Alpha 1_NLGN2" "Alpha 1_CLSTN3" "Alpha 1_FLRT1_ADGRL1"
[88] "Alpha 1_FZD3_LRP6" "Beta 2_GIPR" "Beta 2_ADGRL1"
[91] "Beta 2_FLRT1_ADGRL1" "Beta 1_SORL1" "Beta 1_TNFRSF21"
[94] "Beta 1_ADGRL1" "Beta 1_DAG1" "Beta 1_INSSR"
[97] "Beta 1_ITGAV_ITGB1" "Beta 1_JAM3" "Beta 1_F11R"
[100] "Beta 1_NLGN2" "Beta 1_CLSTN1" "Beta 1_CLSTN3"
[103] "Beta 1_CD44" "Beta 1_ITGAV_ITGB5" "Beta 1_FLRT1_ADGRL1"
[106] "Beta 1_FZD3_LRP6" "Proliferating cells_SORL1" "Proliferating cells_ITGB1_ADGRE5" [109] "Proliferating cells_ITGAV_ITGB1" "Proliferating cells_F11R" "Proliferating cells_ADGRE5"
[112] "Proliferating cells_CD44" "Proliferating cells_ITGAV_ITGB5" "Proliferating cells_ADGRL1"
[115] "Proliferating cells_FLRT1_ADGRL1" "Proliferating cells_FZD3_LRP6"

so some reason, Beta 1_TNFRSF21 will not be plotted in the chordDiagram. Why? Thanks.

mliu86 avatar Aug 12 '24 20:08 mliu86