The function creates a 'four quadrant' MA plot, where the FDR and log2FoldChange thresholds dictate the significant up-regulated category, the significant downregulated category, the significant low regulation category and the non-significant category
Genes of interest are labeled in a rectangle for visibility and will have the same color as the category in which they are in.
The plot is created using ggplot2, to save a plot the ggsave() function is recommended It is also recommended to use the following parameters to save the plot. dpi=300 width=21 height=19 units='cm'
maplot_alt(
DE_res,
genes_of_interest = c(),
filter_choice,
l2FC_thresh = 1,
p_thresh = 0.05,
plot_title = "MA plot"
)The differential expression results to be plotted
A vector containing gene names to be labelled in the plot To not label any genes, leave as default or provide an empty vector.
Either padj or pvalue, the choice will be used to filter for significance
The value used as the log2FoldChange threshold
The value used to establish significance from adjusted pvalue
The title to be give to the plot
None
TS_object<-create_example_object_for_R()
TS_object <- normalize_timeSeries_with_deseq2(time_object=TS_object)
#> converting counts to integer mode
#Perform conditional differential gene expression analysis
TS_object<-conditional_DE_wrapper(TS_object,vignette_run=TRUE)
DE_res<-slot(TS_object,'DE_results')$conditional$IgM_vs_LPS_TP_1$DE_raw_data
ma_plot<-maplot_alt(DE_res = DE_res,filter_choice = 'padj')