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("external_gene_name", "symbol"), slot = 1L, log2 = TRUE, xsLab = xs, color = "black", groupLab = group, batchLab = batch)
dds | DESeq2::DESeqDataSet object or SummarizedExperiment or Matrix or data.frame. |
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xs | Character, colname in colData that will be used as X-axes. |
res | DESeq2::DESeqResults object. |
n | Integer number of genes to plot. |
genes | Character of gene names matching rownames of count data. |
group | Character, colname in colData to color points and add different lines for each level. |
batch | Character, colname in colData to shape points, normally used by batch effect visualization. |
metadata | Metadata in case dds is a matrix. |
ann | Columns in rowData (if available) used to print gene names. |
slot | Name of the slot to use to get count data. |
log2 | Whether to apply or not log2 transformation. |
xsLab | Character, alternative label for x-axis (default: same as xs). |
color | Color to use to plot groups. It can be one color, or a palette
compatible with |
groupLab | Character, alternative label for group (default: same as group). |
batchLab | 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]][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")#>#>