plot_variance: plot variance of counts across samples

In dongzhuoer/rexseek: Matrix Processing in the exSeek Project

Description

plot variance of counts across samples

Usage

plot_cv_density(mat, refer_gene_id = "",
  refer_gene_name = refer_gene_id)

plot_refer_violin(mat, refer_gene_id, refer_gene_name = refer_gene_id)

Arguments

mat	integer matrix. counts
refer_gene_id	character. Ensembl transcript id, add a vertical line for each gene to mark the corresponding CV (on x axis). Only genes in counts matrix would be shown. Usually these genes should be the reference genes you want to use for normalization.
refer_gene_name	character. Transcript name

Details

plot_cv_density() produces density plot of coefficient of variation

plot_refer_violin() produces violin plot of given reference genes's counts (with CV annotated)

Value

ggplot2::ggplot() object.

Examples

# only one gene exist in the matrix
plot_cv_density(sim_mat, suggest_refer$id)
plot_cv_density(sim_mat, suggest_refer$id, suggest_refer$name)

# the name should be the same length as id
plot_cv_density(sim_mat, rownames(sim_mat)[1:6], letters[1:3])
# if only part of the genes have name, you can pass the id of other genes
plot_cv_density(sim_mat, rownames(sim_mat)[1:6], c(letters[1:3], rownames(sim_mat)[4:6]))

# only one gene exist in the matrix
plot_refer_violin(sim_mat, suggest_refer$id)
plot_refer_violin(sim_mat, suggest_refer$id, suggest_refer$name)

# the name should be the same length as id
plot_refer_violin(sim_mat, rownames(sim_mat)[1:6], letters[1:3])
# if only part of the genes have name, you can pass the id of other genes
plot_refer_violin(sim_mat, rownames(sim_mat)[1:6], c(letters[1:3], rownames(sim_mat)[4:6]))

dongzhuoer/rexseek documentation built on Dec. 16, 2019, 3:19 a.m.