KableExtra with conditional font color does not map the right color at the right position

user_3608469 0
Viewed 24

I have a following gene list table in the data.table;

t.mini
    cluster1 cluster15 cluster31
      <fctr>    <fctr>    <fctr>
 1:   Slc6a6      Cd8a    Retnla
 2:   Sema3g     Cd8b1    Cxcl15
 3:  Cyp26b1     Pdcd1   Scgb3a2
 4:    H2-Q6      Cd3g     Sftpb
 5:    Klhl5    Sh2d2a   Scgb1a1
 6:    Dnah8     Cxcr6    Sftpa1
 7:   Tm4sf1      Cd3e      Cbr2
 8: Cdc42bpb     Rgs16     Sftpd
 9:   Cxcl12      Nkg7     Wfdc2
10:   Sptan1    Ms4a4b    Cyp2f2

I would like to output the table with the font color of any Cxcl genes to red by using kableextra, and I came up with a code as follows;

lapply(1:3, function(y) {
  kbl(t.mini) |> 
  kable_classic_2(full_width=F) |> 
  column_spec(column = y, color = fifelse(unlist(t.mini[, lapply(.SD, function(x){grepl(glob2rx("Cx*"), x)})]), "red", "black"))
})

However, the resulting table has red font mapped not only to a wrong gene but only one gene as in this table.

enter image description here

Any pointers will be appreciated.

kableextra kable r
1 Answers

Using cell_spec and transforming the data first before passing it to kbl can work -

library(kableExtra)
library(data.table)

cols <- names(t.mini)
t.mini[, (cols) := lapply(.SD, 
   function(x) cell_spec(x, color = fifelse(grepl('Cxcl', x), 'red', 'black'))), 
       .SDcols = cols]

t.mini |>
  kbl(escape = FALSE) |>
  kable_classic_2(full_width=F)

enter image description here

user_39629140
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