TCGAbiolinks (version 1.2.5)

TCGAvisualize_profilePlot: Profile plot

Description

Displaty the association between cancer subtypes and any kind of clustering.

Usage

TCGAvisualize_profilePlot(data = NULL, groupCol = NULL, subtypeCol = NULL, colors = NULL, filename = NULL, na.rm.groups = FALSE, na.rm.subtypes = FALSE, plot.margin = c(-2.5, -2.5, -0.5, 2), axis.title.size = 1.5, axis.textsize = 1.3, legend.size = 1.5, legend.title.size = 1.5, geom.label.size = 6, geom.label.color = "black")

Arguments

data

A data frame with the cluters and subytpe of cancers

groupCol

Names of tre columns with the cluster information

subtypeCol

Name of the column with the subtype information

colors

Vector of colors to be used in the bars

filename

Name of the file to save the plot, can be pdf, png, svg etc..

na.rm.groups

Remove NA groups? Default = FALSE

na.rm.subtypes

Remove NA subtypes? Default = FALSE

plot.margin

Plot margin for cluster distribution. This can control the size of the bar if the output is not aligned

axis.title.size

axis.title.size

axis.textsize

axis.textsize

legend.size

Size of the legend

legend.title.size

Size of the legend title

geom.label.size

Size of percentage in the left barplot

geom.label.color

Color of percentage in the left barplot

Value

A plot

Examples

while (!(is.null(dev.list()["RStudioGD"]))){dev.off()}
cluster <- c(rep("cluster1",30),
             rep("cluster2",30),
             rep("cluster3",30))
subtype <- rep(c(rep("subtype1",10),
           rep("subtype2",10),
           rep("subtype3",10)),3)
df <- data.frame(cluster,subtype)
TCGAvisualize_profilePlot(data = df, groupCol = "cluster", subtypeCol = "subtype",
                          plot.margin=c(-4.2,-2.5,-0.0,2))
while (!(is.null(dev.list()["RStudioGD"]))){dev.off()}
cluster <- c(rep("cluster1",10),
             rep("cluster2",20),
             rep("cluster3",30),
             rep("cluster4",40))
subtype <- rep(c(rep("subtype1",5),
           rep("subtype2",10),
           rep("subtype3",10)),4)
df <- data.frame(cluster,subtype)
plot <- TCGAvisualize_profilePlot(data = df, groupCol = "cluster", subtypeCol = "subtype",
                          plot.margin=c(-4.2,-2.5,-0.5,2))