plot_line_pattern | R Documentation |
This function creates a line plot of average expression across conditions for a selection of genes, usually to visualise an expression pattern.
plot_line_pattern( tbl, genes = NULL, type = c("Mean Scaled", "Log2 Expression", "Expression"), show.legend = FALSE )
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 |
A matrix of average gene expression per gene in each condition.
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)
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