Plot top genes allowing more variables to color and shape points
degPlot(dds, xs, res = NULL, n = 9, genes = NULL, group = NULL, batch = NULL, metadata = NULL, ann = c("geneID", "symbol"), slot = 1L, log2 = TRUE, xsLab = xs, ysLab = "abundance", color = "black", groupLab = group, batchLab = batch)
DESeq2::DESeqDataSet object or SummarizedExperiment
or Matrix or data.frame. In case of a DESeqDataSet object, always
the normalized expression will be used
Character, colname in colData that will be used as X-axes.
Integer number of genes to plot from the
Character of gene names matching rownames of count data.
Character, colname in colData to color points and add different lines for each level.
Character, colname in colData to shape points, normally used by batch effect visualization.
Metadata in case dds is a matrix.
Columns in rowData (if available) used to print gene names. First
element in the vector is the column name in rowData that matches the
row.names of the
Name of the slot to use to get count data.
Whether to apply or not log2 transformation.
Character, alternative label for x-axis (default: same as xs)
Character, alternative label for y-axis..
Color to use to plot groups. It can be one color, or a palette
Character, alternative label for group (default: same as group).
Character, alternative label for batch (default: same as batch).
ggplot showing the expresison of the genes
data(humanGender) library(DESeq2) idx <- c(1:10, 75:85) dse <- DESeqDataSetFromMatrix(assays(humanGender)[][1:1000, idx], colData(humanGender)[idx,], design=~group) dse <- DESeq(dse)#>#>#>#>#>#>#>#> #>#>#>degPlot(dse, genes = rownames(dse)[1:10], xs = "group")#>#>degPlot(dse, genes = rownames(dse)[1:10], xs = "group", color = "orange")#>#>degPlot(dse, genes = rownames(dse)[1:10], xs = "group", group = "group", color = "Accent")#>#>