LymphGen feature visualization.

Make a heatmap showing the frequency of LymphGen features across a cohort of samples.

Usage

pretty_lymphoplot(
  these_samples_metadata,
  flavour = "with_cnvs.with_sv.with_A53",
  lymphgen_all,
  with_A53 = FALSE,
  show_side_annotation = FALSE,
  verbose = FALSE
)

Arguments

these_samples_metadata

A data frame containing the metadata for your samples (LymphGen result will be subset to the sample_id in this data frame).

flavour

Required if the output of get_lymphgen has not been provided.

lymphgen_all

The list returned by get_lymphgen.

with_A53

Set to FALSE if you are using LymphGen results without A53. Recommended option.

show_side_annotation

Set to TRUE if you want the default ComplexHeatmap annotations on the sides of your heatmap. Default is FALSE.

verbose

Set to TRUE to print helpful messages. Useful for debugging. Default is FALSE (not verbose).

Value

A ComplexHeatmap object

Examples

meta_df = suppressMessages(get_gambl_metadata()) %>% 
  dplyr::filter(seq_type %in% c("genome", "capture")) %>%
     dplyr::filter(pathology == "DLBCL")
pretty_lymphoplot(meta_df, show_side_annotation = TRUE)
#> Joining with `by = join_by(Sample.Name, BTG2)`
#> Joining with `by = join_by(Sample.Name)`
#> Joining with `by = join_by(Sample.Name, SOCS1)`
#> Joining with `by = join_by(Sample.Name)`
#> Joining with `by = join_by(sample_id)`
#> Warning: The input is a data frame-like object, convert it to a matrix.
#> Warning: Note: not all columns in the data frame are numeric. The data frame
#> will be converted into a character matrix.
#> `use_raster` is automatically set to TRUE for a matrix with more than
#> 2000 rows. You can control `use_raster` argument by explicitly setting
#> TRUE/FALSE to it.
#> 
#> Set `ht_opt$message = FALSE` to turn off this message.
#> 'magick' package is suggested to install to give better rasterization.
#> 
#> Set `ht_opt$message = FALSE` to turn off this message.


pretty_lymphoplot(
     meta_df,
     show_side_annotation = TRUE,
     flavour = "with_cnvs.with_sv.no_A53"
)
#> NO A53
#> Joining with `by = join_by(Sample.Name)`
#> Joining with `by = join_by(Sample.Name, BTG2)`
#> Joining with `by = join_by(Sample.Name)`
#> Joining with `by = join_by(Sample.Name, SOCS1)`
#> Running in the mode without A53 ...
#> Joining with `by = join_by(sample_id)`
#> Warning: The input is a data frame-like object, convert it to a matrix.
#> Warning: Note: not all columns in the data frame are numeric. The data frame
#> will be converted into a character matrix.
#> `use_raster` is automatically set to TRUE for a matrix with more than
#> 2000 rows. You can control `use_raster` argument by explicitly setting
#> TRUE/FALSE to it.
#> 
#> Set `ht_opt$message = FALSE` to turn off this message.
#> 'magick' package is suggested to install to give better rasterization.
#> 
#> Set `ht_opt$message = FALSE` to turn off this message.