plot_line_pattern {bulkAnalyseR} | R Documentation |
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 |
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)
[Package bulkAnalyseR version 1.1.0 Index]