obsPlot2: Function obsPlot2

In jrthompson54/DGE.Tools2: A function library to facilitate Differential Gene Expression Analysis

Description

Provides a summary plot (box/violin/points)for each observation (gene), showing data for each experiment group. The plot can optionally include one or more of the following layers: boxplot, violin plot, individual points and/or mean of all points. The layers are built up in the order listed with user settable transparency, colors etc. By default, the Boxplot, Point and Mean layers are active. Also, by default, the plots are faceted. Facet plot can be turned off to return a list of individual ggplot graphics for each gene.

Usage

obsPlot2(
  data,
  plotByCol,
  groupCol,
  valueCol,
  groupOrder = unique(as.character(data[groupCol, , drop = TRUE])),
  boxLayer = TRUE,
  violinLayer = FALSE,
  pointLayer = TRUE,
  meanLayer = TRUE,
  xlab = groupCol,
  ylab = valueCol,
  title,
  boxColor = "grey30",
  boxFill = "deepskyblue3",
  boxAlpha = 0.5,
  boxNotch = FALSE,
  boxNotchWidth = 0.8,
  violinColor = "grey30",
  violinFill = "goldenrod1",
  ViolinAlpha = 0.5,
  pointColor = "grey30",
  pointFill = "dodgerblue4",
  pointShape = 21,
  pointAlpha = 1,
  pointSize = 2,
  pointJitter = 0,
  meanColor = "red2",
  meanFill = "goldenrod1",
  meanShape = 22,
  meanAlpha = 0.7,
  meanSize = 3,
  legenPosition = "right",
  baseFontSize = 12,
  themeStyle = "grey",
  facet = TRUE,
  facetRow,
  xAngle = 30,
  scales = "free_y",
  debug = FALSE
)

Arguments

data	A tidy dataframe of intensity data with row and colnames (required)
plotByCol	Define the column name to separate plots (typically a gene ID column) (required)
groupCol	Define the column name to group boxplots by (typically a replicate group column) (required)
valueCol	Define the column of values for plotting (typically a log intensity measure) (required)
groupOrder	Define the order for the groups in each plot. Should contain values in unique(data$group) listed in the order that you want the groups to appear in the plot. (optional; default = unique(data[groupCol]))
boxLayer	Adds a boxplot layer (Default = TRUE)
violinLayer	Adds a violin layer (Default = FALSE)
pointLayer	Adds a point layer (Default = True)
meanLayer	Adds a mean layer (Default = True)
xlab	X axis label (defaults to groupCol)
ylab	Y axis label (defaults to valueCol)
title	Plot title (optional)
boxColor	Color for the boxplot layer (Default = "grey30")
boxFill	Fill Color for the boxplot layer (Default = "deepskyblue3")
boxAlpha	Transparency for the box layer (Default = 0.5)
boxNotch	turn on/off confidence interval notches on boxplots (Default = FALSE)
boxNotchWidth	Set the width of boxnotches (0-1) (Default = 0.8)
violinColor	Color for the violin layer (Default = "grey30")
violinFill	Fill Color for the violin (Default = "yellow")
pointColor	Color for the point layer (Default = "grey30")
pointFill	Fill color for the point layer (Default = "dodgerblue4")
pointShape	Shape for the point layer (Default = 21; fillable circle)
pointAlpha	Transparency for the box layer (Default = 1)
pointSize	Size of the points (Default = 4)
pointJitter	Amount to jitter the points (Default = 0) Try 0.2 if you have alot of points.
meanColor	Color for the mean layer (Default = "red2")
meanFill	Fill color for the mean layer (Default = "goldenrod1")
meanShape	Shape for the mean layer (Default = 21; fillable circle)
meanAlpha	Transparency for the mean layer (Default = 0.7)
meanSize	Size of the mean points (Default = 3)
baseFontSize	The smallest size font in the figure in points. (Default = 12)
themeStyle	"bw" or "grey" which correspond to theme_bw or theme_grey respectively. Default = bw"
facet	Specifies whether to facet (TRUE) or print individual plots (FALSE) (Default = TRUE)
facetRow	Explicitly set the number of rows for the facet plot. Default behavior will automatically set the columns. (Default = NULL)
xAngle	Angle to set the sample labels on the Xaxis. (Default = 30; Range = 0-90)
scales	Specify same scales or independent scales for each subplot (Default = "free_y"; Allowed values: "fixed", "free_x", "free_y", "free")
debug	Turn on debug mode (default = FALSE)
violinAlpha	Transparency for the box layer (Default = 0.5)

Details

Input is a tidy dataframe of intensity data.

Value

ggplot If Facet=TRUE (default) returns a facetted ggplot object. If facet=FALSE, returns a list of ggplot objects indexed by observation (gene) names.

Author(s)

John Thompson, [e-mail]

Examples

  #simulate some data with row and colnames
  groups <- paste("group", factor(rep(1:4, each=100)), sep="")
  x <- matrix(rnorm(2400, mean=10), ncol=length(groups))
  colnames(x) <- paste("sample", 1:ncol(x), sep="")
  rownames(x) <- paste("gene", 1:nrow(x), sep="")
  #reformat into tidy dataframe
  tidyInt <- tidyIntensity(x,

 #Or get data from a DGEobj with RNA-Seq data
 log2cpm <- convertCount(dgeObj$counts, unit="cpm", log=TRUE, normalize="tmm")
 tidyInt <- tidyIntensity(log2cpm,
                           rowidColname="GeneID",
                           keyColname="Sample",
                           valueColname="Log2CPM",
                           group=dgeObj$design$ReplicateGroup)

  #Facetted boxplot
  obsPlot2(tidyInt, plotByCol="GeneID",
           groupCol = "group",
           valueCol ="Log2CPM",
           pointJitter = 0.1,
           facetRow = 2)

  #Facetted violin plot
  obsPlot2(tidyInt, plotByCol = "GeneID",
           violinLayer = TRUE,
           boxLayer = FALSE,
           groupCol="group",
           valueCol = "Log2CPM",
           pointJitter = 0.1,
           facetRow = 2)

  #Return a list of ggplots for each individual gene
  myplots <- obsPlot2(tidyInt, plotByCol="GeneID",
           groupCol = "group",
           valueCol ="Log2CPM",
           pointJitter = 0.1,
           facet = FALSE)
  #plot one from the list
  myplots[[2]]

jrthompson54/DGE.Tools2 documentation built on May 12, 2021, 8:47 p.m.