degPlot: Plot top genes allowing more variables to color and shape...

Description Usage Arguments Value Examples

View source: R/genePlots.R

Description

Plot top genes allowing more variables to color and shape points

Usage

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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
)

Arguments

dds

DESeq2::DESeqDataSet object or SummarizedExperiment or Matrix or data.frame. In case of a DESeqDataSet object, always the normalized expression will be used from counts(dds, normalized = TRUE).

xs

Character, colname in colData that will be used as X-axes.

res

DESeq2::DESeqResults object.

n

Integer number of genes to plot from the res object. It will take the top N using padj values to order the table.

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. First element in the vector is the column name in rowData that matches the row.names of the dds or count object. Second element in the vector is the column name in rowData that it will be used as the title for each gene or feature figure.

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)

ysLab

Character, alternative label for y-axis..

color

Color to use to plot groups. It can be one color, or a palette compatible with ggplot2::scale_color_brewer().

groupLab

Character, alternative label for group (default: same as group).

batchLab

Character, alternative label for batch (default: same as batch).

Value

ggplot showing the expresison of the genes

Examples

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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")

DEGreport documentation built on Nov. 8, 2020, 7:23 p.m.