is it possible to filter rows of one dataframe based on another dataframe?

here is a basic way to do that:

df_node <- data.frame( id= c("a","b","c","d","e","f","g","h","i"),
                       group= c(1,1,1,2,2,2,3,3,3))

df_link <- data.frame(from = c("a","d","f","i","b"),
                      to =   c("d","f","i","b","h"))


library(dplyr)
df_result <- df_node%>%
       filter(id%in%c(df_link$from,df_link$to))
df_result
# > df_result
# id group
# 1  a     1
# 2  b     1
# 3  d     2
# 4  f     2
# 5  h     3
# 6  i     3

We could use a semi_join:

library(dplyr)

df_node |> 
  semi_join(tibble(id = c(df_link$from, df_link$to)))

Output:

  id group
1  a     1
2  b     1
3  d     2
4  f     2
5  h     3
6  i     3

Here is a oneliner with base R:

df_node[df_node$id %in% unlist(df_link),]

  id group
1  a     1
2  b     1
4  d     2
6  f     2
8  h     3
9  i     3

But you could also use a join:

library(dplyr)

df_uniqueID <- data.frame(id = unique(c(df_link$from,df_link$to)) )
right_join(df_node,df_uniqueID)

Joining, by = "id"
  id group
1  a     1
2  b     1
3  d     2
4  f     2
5  h     3
6  i     3