volcanoDifferentialAtlasExperiment: Generate Volcano plots from analytics data for an Expression...

In ebi-gene-expression-group/bioconductor-ExpressionAtlas: Search, download and visualise datasets from EMBL-EBI Expression Atlas and Single-Cell Expression Atlas

Generate Volcano plots from analytics data for an Expression Atlas experiment

Description

This function generates a volcano plots for an Expression Atlas experiment, from analytics data.

Usage

    volcanoDifferentialAtlasExperiment( df, filename_prefix = "volcano-plot", save_pdf = FALSE, show_plot = TRUE, low_fc_colour = "gray", high_fc_colour = "blue", cutoff = 1, show_volcanoplot_title = TRUE )

Arguments

df	Dataframe in the output format of getAnalysticsDifferentialAtlasExpression.
filename_prefix	Filename for the output volcano plot images. Default is "volcano".
save_pdf	Save PDF file with the heatmap. Default is FALSE.
show_plot	Show plot in the R console. Default is TRUE.
low_fc_colour	Colour palette for the low foldchange. Default is "gray".
high_fc_colour	Colour palette for the high foldchange. Default is "blue".
cutoff	cutoff for the foldchange. Default is 1.
show_volcanoplot_title	Whether to show a title in the volcano plot. Default is TRUE.

Value

Image file(s) with the generated volcano plots.

Examples

    
    # Download the differential expression analytics data for experiment E-MTAB-10104
    mtab10104_dea <- getAnalysticsDifferentialAtlasExpression( "E-MTAB-10104" )

    # Generate volcano plots with default parameters
    volcanoDifferentialAtlasExperiment( mtab10104_dea )

    # Check if the image files were created
    # file.exists("heatmap.pdf")

    # Generate volcano plots with custom parameters
    volcanoDifferentialAtlasExperiment( mtab10104_dea, "E-MTAB-10104", FALSE, TRUE, "Gray", "Blue", 1, TRUE )

    # Check if the image files were created
    # file.exists("E-MTAB-4045-cpm-heatmap.pdf")

ebi-gene-expression-group/bioconductor-ExpressionAtlas documentation built on July 4, 2025, 12:53 a.m.