View source: R/vis_pancan_value.R
vis_toil_TvsN | R Documentation |
Visualize Pan-cancer TPM (tumor (TCGA) vs Normal (TCGA & GTEx))
vis_toil_TvsN( Gene = "TP53", Mode = c("Boxplot", "Violinplot"), data_type = "mRNA", Show.P.value = TRUE, Show.P.label = TRUE, Method = c("wilcox.test", "t.test"), values = c("#DF2020", "#DDDF21"), TCGA.only = FALSE, draw_quantiles = c(0.25, 0.5, 0.75), trim = TRUE, include.Tumor.only = FALSE )
Gene |
a molecular identifier (e.g., "TP53") or a formula specifying
genomic signature ( |
Mode |
"Boxplot" or "Violinplot" to represent data |
data_type |
choose gene profile type, including "mRNA", "transcript", "protein", "mutation", "cnv" (-2, -1, 0, 1, 2), "cnv_gistic2", "methylation", "miRNA". |
Show.P.value |
|
Show.P.label |
|
Method |
default method is wilcox.test |
values |
the color to fill tumor or normal |
TCGA.only |
include samples only from TCGA dataset |
draw_quantiles |
draw quantiles for violinplot |
trim |
whether trim the violin |
include.Tumor.only |
if |
a ggplot
object
## Not run: p <- vis_toil_TvsN(Gene = "TP53", Mode = "Violinplot", Show.P.value = FALSE, Show.P.label = FALSE) p <- vis_toil_TvsN(Gene = "TP53", Mode = "Boxplot", Show.P.value = FALSE, Show.P.label = FALSE) ## End(Not run)
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