I have a simple problem of trying to produce an HTML file with rmarkdown. I want to include a table which has one column which has a long list of genes. All I want to do is set the column width of each column, both columns will require wrapping.
I have gone with pander and it seems to be working when called in R, but when I create the HTML only the first row is included in the table.
pander(df, split.cells = c(30,70), split.table = Inf)
Below is the HTML output any ideas what is happening?
dput(df)
structure(c("Cell Cycle, Mitotic", "Cell Cycle", "Adaptive Immune System",
"Mitotic G1-G1/S phases", "Cytokine Signaling in Immune system",
"G1/S Transition", "DNA Replication", "G2/M Checkpoints", "Activation of ATR in response to replication stress",
"S Phase", "CDKN2A, SKP2, CCNE1, NCAPD2, LPIN1, MCM10, TFDP1, NUP155, MCM3, E2F3, OPTN, RFC4, NUP160, CENPN, TFDP2, CCNA1, NUP153, PSMB10, PRKCA, CKAP5, KIF2C, PSME4, GINS4, FOXM1, SEC13, RB1, MCM4, MCM5, CCNA2, PSMB9, RFC3, NCAPG2, CDC7, MCM7, NUP205, CENPA, PRKCB, BIRC5, SMC2, BUB1, CDCA8, PRIM2, NDC80, CDKN2C, PLK1, PPP1CB, CETN2, CEP57, NUP50, PSME1, CCNE2, PSMB8, NCAPH2, VRK1, CDC20, PCM1, MCM2, E2F5, TUBA4A, PSMB2, CDT1, SMC4, ORC1, CUL1, AURKB, PSMD2, CDC25B, KIF18A, UBE2D1, RFC2, TUBG2, SMC1A, PSMB4, NCAPD3, BTRC, CDK6, DNA2, NUP93, POLD1, SPDL1, RBL1, CENPI, PCNA, MCM6, NUP62, POLE2, SKA1, CLASP2, ARPP19, CKS1B, AKAP9, PSMC2, WAPL, BORA, DBF4, CENPF, PLK4, NEK2, SKP1, ORC6, NUMA1, PAFAH1B1, TYMS, KIF23, ZWILCH, FBXO5, FEN1, PSMF1, RRM2",
"CDKN2A, SFN, SKP2, CCNE1, NCAPD2, LPIN1, MCM10, TFDP1, NUP155, CHEK1, MCM3, E2F3, OPTN, RFC4, NUP160, CENPN, TFDP2, CCNA1, STAG3, NUP153, PSMB10, PRKCA, CKAP5, KIF2C, PSME4, GINS4, FOXM1, SEC13, RB1, MCM4, MCM5, CCNA2, PSMB9, RFC3, NCAPG2, CDC7, MCM7, NUP205, CENPA, HSPA2, PRKCB, BIRC5, SMC2, BUB1, CDCA8, PRIM2, NDC80, CDKN2C, PLK1, PPP1CB, CETN2, CEP57, NUP50, PSME1, CCNE2, PSMB8, MLH1, NCAPH2, VRK1, CDC20, PCM1, MCM2, E2F5, TUBA4A, MRE11A, PSMB2, CDT1, SMC4, ORC1, CUL1, AURKB, PSMD2, CHEK2, CDC25B, KIF18A, UBE2D1, RFC2, TUBG2, SMC1A, HJURP, PSMB4, NCAPD3, HUS1, BTRC, BLM, YWHAB, CDK6, DNA2, NUP93, POLD1, SPDL1, RBL1, CENPI, YWHAQ, PCNA, MCM6, RAD1, NUP62, BRCA2, POLE2, SKA1, CLASP2, ARPP19, CKS1B, AKAP9, PSMC2, WAPL, SUN2, BORA, DBF4, CENPF, PLK4, NEK2, SKP1, ORC6, NUMA1, PAFAH1B1, TYMS, KIF23, ZWILCH, FBXO5, FEN1, MIS18A, PSMF1, RRM2",
"CTSV, HLA-DOB, PLCG2, NCK1, DYNC1I1, ERBB4, TAP1, LYN, TAP2, ICAM1, RAC1, CYBB, ICOS, CD19, NFKBIE, PSMB10, SOS1, YES1, SELL, KIF2C, AGO1, ITPR1, ITK, PSME4, CD247, SEC13, INPP5D, CD79A, PIK3CD, RIPK2, HLA-F, PSMB9, CD8B, CD96, CTSS, LCK, NCF4, FYB, RASGRP2, PRKCB, ZAP70, PTPRC, TRAT1, LILRB2, PVR, ITPR3, CD8A, CD40, PRKCQ, CD3D, RASGRP3, LCP2, KLRD1, ITGB5, CRTAM, MALT1, CD79B, PSME1, BTK, PSMB8, VAV1, PDGFRA, PSMB2, PAK3, NRAS, CUL1, HLA-DMB, AP1M2, PSMD2, KIF18A, SYK, VCAM1, CD28, NCF2, CD86, CD3E, CD3G, EGFR, FGFR3, PSMB4, LILRB1, BTRC, YWHAB, CD4, KIF3C, PAK2, SEC24B, IKBKB, NPEPPS, RAPGEF3, ICAM2, ICOSLG, ITGB7, DCTN4, PSMC2, KIF3A, RAPGEF4, CSK, CTLA4, FYN, SKP1, ERBB3, KIF23, NFKBIB, ITGB2, FCGR1B, PSMF1",
"CDKN2A, SKP2, CCNE1, MCM10, TFDP1, MCM3, E2F3, TFDP2, CCNA1, PSMB10, RB1, MCM4, MCM5, PSMB9, CDC7, MCM7, PRIM2, CDKN2C, PSME1, CCNE2, PSMB8, MCM2, E2F5, PSMB2, CDT1, ORC1, CUL1, PSMD2, PSMB4, CDK6, RBL1, PCNA, MCM6, POLE2, CKS1B, PSMC2, DBF4, SKP1, ORC6, TYMS, FBXO5, PSMF1, RRM2",
"IRAK1, IL1R2, IL6ST, NUP155, IFNG, IRF1, CSF2RB, LYN, ICAM1, IRF8, MAP2K4, NUP160, ADAM17, SOCS2, IRF4, SOCS1, NUP153, SOS1, IL2RG, PTPN2, INPP5D, PIK3CD, IL1RAP, RIPK2, GBP1, HLA-F, TRIM38, PML, NUP205, IFNGR1, CIITA, MYD88, HERC5, MID1, ISG20, IFNAR2, IL7, NUP50, PSMB8, CASP1, CSF2RA, VAV1, CAMK2B, GBP2, KPNA4, NRAS, STAT1, CUL1, SYK, PRLR, IL2RB, VCAM1, IL7R, USP18, CISH, MX2, IL2RA, IL6R, BTRC, YWHAB, LGALS9, NUP93, PTAFR, KPNA3, MAPK1, IKBKB, RSAD2, NUP62, OASL, EIF4E2, SAMHD1, TRIM8, KPNA5, FYN, SKP1, FCGR1B",
"SKP2, CCNE1, MCM10, TFDP1, MCM3, CCNA1, PSMB10, RB1, MCM4, MCM5, PSMB9, CDC7, MCM7, PRIM2, PSME1, CCNE2, PSMB8, MCM2, PSMB2, CDT1, ORC1, CUL1, PSMD2, PSMB4, PCNA, MCM6, POLE2, CKS1B, PSMC2, DBF4, SKP1, ORC6, TYMS, FBXO5, PSMF1, RRM2",
"MCM10, MCM3, RFC4, PSMB10, PSME4, GINS4, RB1, MCM4, MCM5, PSMB9, RFC3, CDC7, MCM7, PRIM2, PSME1, PSMB8, MCM2, PSMB2, CDT1, ORC1, PSMD2, RFC2, PSMB4, DNA2, POLD1, PCNA, MCM6, POLE2, PSMC2, DBF4, ORC6, FEN1, PSMF1",
"SFN, MCM10, CHEK1, MCM3, RFC4, MCM4, MCM5, RFC3, CDC7, MCM7, MCM2, ORC1, CHEK2, RFC2, HUS1, YWHAB, YWHAQ, MCM6, RAD1, DBF4, ORC6",
"MCM10, CHEK1, MCM3, RFC4, MCM4, MCM5, RFC3, CDC7, MCM7, MCM2, ORC1, RFC2, HUS1, MCM6, RAD1, DBF4, ORC6",
"SKP2, MCM3, RFC4, PSMB10, PSME4, GINS4, RB1, MCM4, MCM5, PSMB9, RFC3, MCM7, PRIM2, PSME1, PSMB8, MCM2, PSMB2, CDT1, ORC1, CUL1, PSMD2, RFC2, SMC1A, PSMB4, DNA2, POLD1, PCNA, MCM6, POLE2, CKS1B, PSMC2, WAPL, SKP1, ORC6, FEN1, PSMF1"
), .Dim = c(10L, 2L), .Dimnames = list(c("1", "2", "3", "4",
"5", "6", "7", "8", "9", "10"), c("Pathway", "GeneID")))
view of R console showing splitting working.
