Visualize Correlation between Gene and Tumor Stemness

Usage

vis_gene_stemness_cor(
  Gene = "TP53",
  cor_method = "spearman",
  data_type = "mRNA",
  Plot = "TRUE",
  opt_pancan = .opt_pancan
)

Arguments

Gene: a molecular identifier (e.g., "TP53") or a formula specifying genomic signature ("TP53 + 2 * KRAS - 1.3 * PTEN").
cor_method: correlation method
data_type: choose gene profile type, including "mRNA", "transcript", "protein", "mutation", "cnv", "methylation", "miRNA".
Plot: output the plot directly, default 'TRUE'
opt_pancan: specify one dataset for some molercular profiles

Examples

if (FALSE) { # \dontrun{
p <- vis_gene_stemness_cor(Gene = "TP53")
p
} # }
## To generate a radar plot, uncomment the following code
# pdata <- p$data %>%
#   dplyr::mutate(cor = round(cor, digits = 3), p.value = round(p.value, digits = 3))
#
# df <- pdata %>%
#   select(cor, cancer) %>%
#   pivot_wider(names_from = cancer, values_from = cor)
#
# ggradar::ggradar(
#   df[1, ],
#   font.radar = "sans",
#   values.radar = c("-1", "0", "1"),
#   grid.min = -1, grid.mid = 0, grid.max = 1,
#   # Background and grid lines
#   background.circle.colour = "white",
#   gridline.mid.colour = "grey",
#   # Polygons
#   group.line.width = 1,
#   group.point.size = 3,
#   group.colours = "#00AFBB") +
#   theme(plot.title = element_text(hjust = .5))