Description Usage Arguments Details
Generate a volcano plot of genes from a differential expression (limma) analysis, with point inclusion and color based on membership in modules from a WGCNA analysis. This plot can be output to a plotting window, or to a pdf. Points can be selected for inclusion based on their connectivity to the module eigengene (kME). Points can be labeled with gene names, and the points to be labeled can be set based on an ellipse oriented to the x- and y-axes.
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topGenes |
a data frame, typically the output of a call to |
gene_modules |
a data frame containing the gene module memberships. Must contain, at minimum, columns for |
plotdims |
a numeric vector, the size (in inches) of the plotting object. Either the size of the pdf, or the size of the plotting window. |
fc_cut |
numeric, the (absolute value) log2 fold-change threshold for determining significance of genes. This value is also plotted as vertical dotted lines. |
p_cut |
numeric, the p-value threshold for determining significance of genes. This value is also plotted as a horizontal dotted line. |
x_lim, y_lim |
numeric vectors, the lower and upper limits of the plotting space along the x- and y-axes. Passed to |
gene_labs |
logical, whether to include gene labels for genes with extreme logFC and p-value. If |
x_cut, y_cut |
numeric, the radii of the labeling ellipse along the x- and y-axes. Genes with values outside the ellipse are labeled with gene names. Default to 0, which results in all genes being labeled. |
point_order |
character string, specifying how to order the points. Currently accepted values are "random", which randomizes the order of the points, and "input", which send the points to ggplot as they are in the input data frame. Defaults to "random". |
Genes with kME_color_assigned > kME_cut
are plotted. Colors of points are determined by the values of color_assigned
; if different colors are preferred, these values must be modified prior to calling plot_WGCNA_module_volcano_2var
.
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