Book fails to build with new flow chapter

[hammer]

The problem seems to be in the plot-gating-template chunk in Flow.Rmd. The book builds fine if I comment out this chunk and everything below it.

Here's the masking caused by that cell:

Adding population:Live
Adding population:Lymphocytes
Adding population:Singlets
Adding population:gdTCells
Adding population:abTCells
Adding population:maiTCells

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:dplyr':

    combine, intersect, setdiff, union

The following object is masked from 'package:fs':

    path

The following object is masked from 'package:flowCore':

    normalize

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    anyDuplicated, append, as.data.frame, basename, cbind,
    colMeans, colnames, colSums, dirname, do.call, duplicated,
    eval, evalq, Filter, Find, get, grep, grepl, intersect,
    is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
    Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which, which.max,
    which.min

Attaching package: 'graph'

The following object is masked from 'package:stringr':

    boundary

The error I get when this chunk is left uncommented:

label: pgse2770tidy (with options) 
List of 1
 $ dependson: chr "pgse2770"

Quitting from lines 325-331 (learning-about-t-cells-through-data.Rmd) 
Error in mutate_impl(.data, dots) : 
  Evaluation error: argument "graph" is missing, with no default.
Calls: <Anonymous> ... <Anonymous> -> mutate -> mutate.tbl_df -> mutate_impl
In addition: There were 49 warnings (use warnings() to see them)
Execution halted

Exited with status 1.

[hammer]

Trying out the "Knit and Merge" strategy mentioned at https://bookdown.org/yihui/bookdown/new-session.html

[hammer]

Knit and Merge worked!

[hammer]

Well, almost: paths to figures are now busted. Need to sort that out.