Sample-level Circos Plot

Plot a sample-centric circos overview.

plot_sample_circos(
  this_sample_id,
  sv_df,
  cnv_df,
  ssm_df,
  include_sv = TRUE,
  include_ssm = FALSE,
  legend_metadata_columns,
  legend_metadata_names = c(),
  include_cnv = TRUE,
  this_projection = "grch37",
  this_seq_type = "genome",
  chrom_list,
  label_genes,
  auto_label_sv = FALSE
)

Arguments

this_sample_id

Sample ID for the sample to plot.

sv_df

Optional data frame of SVs. If not provided this function will run get_manta_sv to retrieve SVs.

cnv_df

Optional data frame of CNVs. If not provided, this function will run get_sample_cn_segments to retrieve CNVs.

ssm_df

This parameter does not do anything yet. Maybe it was meant to be implemented.

include_sv

Default TRUE. (does not do anything yet).

include_ssm

Defaul FALSE. (does not do anything yet).

legend_metadata_columns

Column names from metadata

legend_metadata_names

List of metadata names to be plotted.

include_cnv

Default TRUE. (does not do anything yet).

this_projection

The selected projection, default is grch37 and it's the only supported peojection.

this_seq_type

Seq type for returned CN segments. One of "genome" (default) or "capture".

chrom_list

List of chromosomes to be plotted. If not stated, chr1-22+X will bes used.

label_genes

Gene labels (df, list or what type?)

auto_label_sv

Default is FALSE

Value

Nothing

Details

This function takes a sample ID in the this_sample_id parameter. Optionally, the user can supply already loaded data frames (SV, CNV, SSM) with the sv_df, cnv_df and ssm_df parameters. Convenient Boolean parameteers are also avaialble for restricting the plot to specific mutation types (include_sv, include_cnv, and include_ssm).

Examples

plot_sample_circos(this_sample_id = "13-38657_tumorB",
                   legend_metadata_columns = c("pathology",
                                               "lymphgen",
                                               "COO_consensus",
                                               "DHITsig_consensus",
                                               "bcl2_ba",
                                               "myc_ba"),
                   legend_metadata_names = c("pathology",
                                             "LymphGen",
                                             "COO",
                                             "DHITsig",
                                             "BCL2",
                                             "MYC"),
                   chrom_list = c("chr2",
                                  "chr3",
                                  "chr8",
                                  "chr14",
                                  "chr18"))
#> WARNING! No SV calls found in flat-file for: 171116-PL02
#> WARNING! No SV calls found in flat-file for: 171447-PL01
#> WARNING! No SV calls found in flat-file for: 171451-PL01
#> [1] ">>>>>>>"
#> finding colour forDLBCL
#> [1] "<<<<<<<"
#> [1] "using alias to look up colours for pathology"
#> using pathology for pathology
#> adding:#479450
#> [1] ">>>>>>>"
#> finding colour forST2
#> [1] "<<<<<<<"
#> [1] "using alias to look up colours for lymphgen"
#> using lymphgen for lymphgen
#> adding:#C7371A
#> [1] ">>>>>>>"
#> finding colour forGCB
#> [1] "<<<<<<<"
#> [1] "using alias to look up colours for COO_consensus"
#> using coo for COO_consensus
#> adding:#F58F20
#> [1] ">>>>>>>"
#> finding colour forDHITsig-IND
#> [1] "<<<<<<<"
#> [1] "using alias to look up colours for DHITsig_consensus"
#> using coo for DHITsig_consensus
#> adding:#003049
#> [1] ">>>>>>>"
#> finding colour forPOS
#> [1] "<<<<<<<"
#> [1] "using alias to look up colours for bcl2_ba"
#> using pos_neg for bcl2_ba
#> adding:#c41230
#> [1] ">>>>>>>"
#> finding colour forPOS
#> [1] "<<<<<<<"
#> [1] "using alias to look up colours for myc_ba"
#> using pos_neg for myc_ba
#> adding:#c41230
#>       DLBCL        <NA>         GCB DHITsig-IND         POS         POS 
#>   "#479450"          NA   "#F58F20"   "#003049"   "#c41230"   "#c41230" 
#> Error in gpar(fill = cols): could not find function "gpar"