plot_line_pattern: Create a line plot of average expression across conditions

In bulkAnalyseR: Interactive Shiny App for Bulk Sequencing Data

Create a line plot of average expression across conditions

Description

This function creates a line plot of average expression across conditions for a selection of genes, usually to visualise an expression pattern.

Usage

plot_line_pattern(
  tbl,
  genes = NULL,
  type = c("Mean Scaled", "Log2 Expression", "Expression"),
  show.legend = FALSE
)

Arguments

tbl	the output of calculate_condition_mean_sd_per_gene
genes	gene names to use for the output; if NULL (the default), all genes will be used
type	whether the expression values should be scaled using their mean (default), log-transformed, or not adjusted for the plot
show.legend	whether to show the gene names in the legend; should be avoided in many genes are plotted

Value

A matrix of average gene expression per gene in each condition.

Examples

expression.matrix.preproc <- as.matrix(read.csv(
  system.file("extdata", "expression_matrix_preprocessed.csv", package = "bulkAnalyseR"), 
  row.names = 1
))[1:500,]

condition <- factor(rep(c("0h", "12h", "36h"), each = 2))
tbl <- calculate_condition_mean_sd_per_gene(expression.matrix.preproc[1:10, ], condition)
plot_line_pattern(tbl)

bulkAnalyseR documentation built on Dec. 28, 2022, 2:04 a.m.