Visualize Gene-Gene Correlation in TCGA
Usage
vis_pcawg_gene_cor(
Gene1 = "CSF1R",
Gene2 = "JAK3",
data_type1 = "mRNA",
data_type2 = "mRNA",
cor_method = "spearman",
purity_adj = TRUE,
use_log_x = FALSE,
use_log_y = FALSE,
use_regline = TRUE,
dcc_project_code_choose = "BLCA-US",
use_all = FALSE,
filter_tumor = TRUE,
alpha = 0.5,
color = "#000000",
opt_pancan = .opt_pancan
)Arguments
- Gene1
a molecular identifier (e.g., "TP53") or a formula specifying genomic signature (
"TP53 + 2 * KRAS - 1.3 * PTEN").- Gene2
a molecular identifier (e.g., "TP53") or a formula specifying genomic signature (
"TP53 + 2 * KRAS - 1.3 * PTEN").- data_type1
choose gene profile type for the first gene, including "mRNA","transcript","methylation","miRNA","protein","cnv_gistic2"
- data_type2
choose gene profile type for the second gene, including "mRNA","transcript","methylation","miRNA","protein","cnv_gistic2"
- cor_method
correlation method
- purity_adj
whether performing partial correlation adjusted by purity
- use_log_x
if
TRUE, log X values.- use_log_y
if
TRUE, log Y values.- use_regline
if
TRUE, add regression line.- dcc_project_code_choose
select project code.
- use_all
use all sample, default
FALSE.- filter_tumor
whether use tumor sample only, default
TRUE- alpha
dot alpha.
- color
dot color.
- opt_pancan
specify one dataset for some molercular profiles