james-2879 / tcgadataanalysis Goto Github PK

1. source("TCGA_functions.R")
2. TCGA_initialize(user, alternatePath = FALSE, projects = FALSE, unit = FALSE)
3. TCGA_specific_plot_function() # function docs below

Done.

1. May need to define whole path to TCGA_functions.R.
2. User is required to specify data mount point on Ubuntu file system. If your data isn't at /mnt/user/..., then specify your path using TCGA_initialize(alternatePath = "/path/.../tcga/data/).
3. Projects may be parsed as a vector.
4. Whichever function you choose; functions may have both required and optional arguments.

1. source("/home/james.swift/Documents/TCGAtools/functions.R")
2. TCGA_initialize(user = "james.swift", projects = "TCGA-UVM", unit = "TPM")
3. TCGA_survival_plot_(gene = "CD4", indication = "TCGA-UVM", unit = "TPM")

All functions that start with TCGA_ are desgined to be called, but any functions that start with private_TCGA_ should not be, these should only be called by TCGAtools functions.

Any arguments assigned a boolean value below are displaying the default values, and are therefore optional.

TCGA_survival_plot(gene, indication, unit, riskTable = TRUE, censorPlot = TRUE)

For now only one gene, indication, unit per each function call.

TCGA_correlation_plot(genes, indications, unit, sampleType, correlation = TRUE, regression = TRUE)

TCGA_expression_plot_sample(genes, indications, sampleTypes, unit)

TCGA_expression_cutoff(type, cutoff, genes, indications, sampleTypes, unit)

• Type: "boxplot" or "density"
• Cutoff: Float between 0 and 1

TCGA_heatmap(scaled = TRUE, genes, indication, unit)

• Scaled: Scale by gene or by patient (sample).

themes.R

General stylistic attributes for ggplots.