Radar plot usage in R - Visualize Correlation between Gene and Tumor Stemness

[quiquemedina]

Hi there!

In RStudio help and the Package ‘UCSCXenaShiny’ manual (page 31), the command below does not plot a radar plot but a histogram. However, in the app it does

Usage is:
vis_gene_stemness_cor(
Gene = "TP53",
cor_method = "spearman",
data_type = "mRNA",
Plot = "TRUE"
)

I installed ggradar to create radar charts using ggplot2 but fell to reproduce a plot.
I want to ask you for a syntax example for the usage of UCSCXenaShiny stemness in R with a radar plot as output.

[Byronxy]

Hi quiquemedina,
Currently we don't package the radar plot as a function. Here I provide the code about how to plot a radar plot. This is the same way as the shiny app does. Hope this could help you!
Below is the code:

library(UCSCXenaShiny)
library(ggradar)

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

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))

[quiquemedina]

Thank you so much for your (as always) expedited resolution and help.
Enrique.