Gene Cloud Plot
prettyGeneCloud.RdMake a word cloud of gene names from a MAF file based on mutation frequency.
prettyGeneCloud(
maf_df,
these_genes,
other_genes,
these_genes_colour = "#B2DF8A",
other_genes_colour = "#bc42f5",
colour_index
)Arguments
- maf_df
A MAF-format data frame containing the mutations you want to summarize in a gene word cloud
- these_genes
An optional vector of gene symbols (defaults to all lymphoma genes)
- other_genes
An optional second vector of gene symbols to include in your cloud in a second colour
- these_genes_colour
Specify the hex code of a colour to use for the first set of genes
- other_genes_colour
Specify another hex code of a colour to use for the second set of genes
- colour_index
Optional named character vector with a name for each gene in these_genes and a colour as the value
Value
data frame with counts for each gene
Details
Create a wordcloud from an incoming MAF. Required parameter is maf_df.
Optional parameters are these_genes, other_genes, these_genes_colour, other_genes_colour and colour_index.
If no genes are supplied when calling the function, this function will default to all lymphoma genes.
Examples
#get all coding SSM
maf = get_coding_ssm(seq_type = "genome")
#> reading from: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf
#> mutations from 1652 samples
#> after linking with metadata, we have mutations from 1646 samples
#get gene symbols from MAF
maf_genes = dplyr::filter(maf, Hugo_Symbol != "Unknown")
maf_genes_chr1 = dplyr::filter(maf_genes, Chromosome == "1")
my_genes = maf_genes_chr1$Hugo_Symbol
#build wordcloud
prettyGeneCloud(maf_df = maf, these_genes = my_genes)
#> Hugo_Symbol n
#> 1 A3GALT2 4
#> 2 AADACL3 6
#> 3 AADACL4 7
#> 4 ABCA4 30
#> 5 ABCB10 5
#> 6 ABCD3 5
#> 7 ABL2 8
#> 8 AC096677.1 3
#> 9 AC119673.1 1
#> 10 ACADM 6
#> 11 ACAP3 7
#> 12 ACBD3 7
#> 13 ACBD6 1
#> 14 ACOT11 8
#> 15 ACOT7 5
#> 16 ACP6 4
#> 17 ACTA1 5
#> 18 ACTL8 3
#> 19 ACTN2 15
#> 20 ACTRT2 1
#> 21 ADAM15 8
#> 22 ADAM30 9
#> 23 ADAMTS4 5
#> 24 ADAMTSL4 22
#> 25 ADAMTSL4-AS1 6
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#> # A tibble: 2,006 × 2
#> Hugo_Symbol n
#> <fct> <int>
#> 1 AC119673.1 1
#> 2 ACBD6 1
#> 3 ACTRT2 1
#> 4 AGTRAP 1
#> 5 AHCYL1 1
#> 6 AKIRIN1 1
#> 7 AL109927.1 1
#> 8 AL136115.1 1
#> 9 AL138847.1 1
#> 10 AL139147.1 1
#> # ℹ 1,996 more rows