boxplot_genedata: Fast way to draw boxplot for gene expression

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

boxplot_genedata provide fast way to draw boxplot for gene expression based on gene expression matrix and design object

Usage

boxplot_genedata(select.genes, design, expr.matrix, convert = T,
  type = c("facet", "normal")[1], contrast = "N.status",
  contrast.list = c("N0", "Np"), genes.levels = NULL, palette = NULL,
  point.alpha = 0.5, box.alpha = 1, method = "wilcox.test",
  x.title = NULL, y.title = NULL, legend.position = c(0.9, 0.9),
  cut = F, ncut = 2, width = 12, height = 10, names = "love")

Arguments

select.genes	the genes you want to plot
design	the design object(data of clinical features)
expr.matrix	expression matrix of genes
convert	Whether to convert Ensembl id as symbols.Default is convert = T.Note that if you use common names as genes(like miRNAs names),please set convert = F.
type	the style of boxplot.One of "facet" and "normal".
contrast	the colnames of contrast value.Like "N.status".
contrast.list	the components of contrast.Like c("N0","Np")
genes.levels	the level of genes.Default is NULL,and it's recommanded that you set a self-defined levels for better visualization.
palette	the color of genes ploted.Default is NULL.
point.alpha	the color density of point
box.alpha	the color density of box
method	the method of P value for comparision.Default is "wilcox.test".See also method of compare_means function.
x.title	the names of x axis of plot
y.title	the names of y axis of plot
cut	whether to cut plot.If the number of genes is very much,it is recommanded to set cut = T for better visualization.
ncut	the number of cut strategy.Only available when cut = T.Default is 2.
width	the width of plot
height	the height of plot
names	part name of the saved plot

Details

the names of genes shold be Ensembl id.

Author(s)

Weibin Huang<[e-mail]>

See Also

compare_means

Examples

library(lucky)
data("rna.tpm",package = "lucky")
data("rna.design",package = "lucky")
p <- boxplot_genedata(select.genes = c("ENSG00000004478",
                                       "ENSG00000000457"),
                      design = rna.design,
                      expr.matrix = log2(rna.tpm + 1),
                      contrast = "condition",
                      contrast.list = c("normal","tumor"),
                      genes.levels = NULL,
                      palette=NULL,
                      point.alpha = 0.5,
                      box.alpha = 1,
                      method = "wilcox.test",
                      x.title="Genes",
                      y.title="The Expression of Genes(log TPM)",
                      cut = F,
                      width = 12,height = 10,
                      names = "love")
## See plot of genes expression
print(p$plot)

## See meta data of genes expression
View(p$metadata)

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.