venn_diagram: Venn diagram of differential expression genes list

In Facottons/DOAGDC: A Package to Download, Organize and Analyze Genomic Data Commons (GDC) Data

Description

Venn diagram of differential expression genes list

Usage

venn_diagram(
  final_data,
  n_pack = 3,
  package_names,
  pair_name = "G2_over_G1",
  width = 2000,
  height = 2000,
  res = 300,
  unit = "px",
  colors = c("green", "blue", "red"),
  venn_diagram_imagetype = "png",
  work_dir,
  fc_cutoff = 2,
  fdr_cutoff = 0.05,
  env
)

Arguments

final_data	A character string indicating the name of which diferential expression package should be used to get the statistical values in the final list. The default is "EBSeq".
n_pack	A numerical value indicating the number of expression analysis to be used in venn diagram. It is expected the number 2 or 3. The default is 3.
package_names	A character vector indicating the names of at least two diferential expression packages used in previous steps: "DESeq2", "edgeR", "DESeq2, or "All".
pair_name	A character string indicating which condition name should be used. When there are only two groups the default is "G2_over_G1".
width	Graphical parameters. See par for more details. As default width = 2000, height = 1500, res = 300 and unit = "px".
height	Graphical parameters. See par for more details. As default width = 2000, height = 1500, res = 300 and unit = "px".
res	Graphical parameters. See par for more details. As default width = 2000, height = 1500, res = 300 and unit = "px".
unit	Graphical parameters. See par for more details. As default width = 2000, height = 1500, res = 300 and unit = "px".
colors	A character vector indicating the colors to be used in the venn diagram. The default is c('green', 'blue', "red").
venn_diagram_imagetype	A character string indicating the venn_diagram_imagetype (e.g. "tiff", "png" or "svg"). The default is "png".
work_dir	A character string specifying the path to work directory.
fc_cutoff	Numerical value indicating the maximum value for Fold Change '(FC). The default is 2.
fdr_cutoff	Numerical value indicating the maximum value for FDR values. The default is 0.05.
env	A character string containing the environment name that should be used. If none has been set yet, the function will create one in global environment following the standard criteria: 'tumor_data_base_data_type_tumor_data' or 'tumor_data_base_data_type_both_data' (for tumor and not tumor data in separated matrices).

Value

a list of differentially expressed genes in common between two or three differential expression analysis packages.

Examples

library(DOAGDC)

# data already downloaded using the 'download_gdc' function
concatenate_expression("gene",
    name = "HIF3A",
    data_base = "legacy",
    tumor = "CHOL",
    work_dir = "~/Desktop"
)

# separating gene HIF3A expression data patients in two groups
groups_identification_mclust("gene", 2,
    name = "HIF3A",
    modelName = "E",
    env = CHOL_LEGACY_gene_tumor_data,
    tumor = "CHOL"
)

# load not normalized data
concatenate_expression("gene",
    normalization = FALSE,
    name = "HIF3A",
    data_base = "legacy",
    tumor = "CHOL",
    env = CHOL_LEGACY_gene_tumor_data,
    work_dir = "~/Desktop"
)

# start DE analysis
dea_edger(
    name = "HIF3A",
    group_gen = "mclust",
    env = CHOL_LEGACY_gene_tumor_data
)

dea_ebseq(
    pair_name = "G2_over_G1",
    rounds = 2,
    name = "HIF3A",
    group_gen = "mclust",
    env = CHOL_LEGACY_gene_tumor_data
)

# run the Venn diagram
venn_diagram(
    final_data = "edgeR",
    n_pack = 2,
    package_names = c("EBSeq", "edgeR"),
    env = CHOL_LEGACY_gene_tumor_data
)

Facottons/DOAGDC documentation built on April 7, 2020, 3:17 a.m.