logRatioPlot: Function logRatioPlot

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

Description

Intended to plot a set of contrast results, one plot for each gene of interest. Input is a tidy datafile constructed from topTable output and requires logFC, CI.L and CI.R columns as well as a gene identifier of choice. Outputs a ggplot object facetted by the facetColname or a list of individual ggplots, one for each facetColname value (typically gene).

Usage

logRatioPlot(
  data,
  facetColname,
  xColname,
  yColname = "logFC",
  CI.R_colname = "CI.R",
  CI.L_colname = "CI.L",
  xOrder = unique(as.character(data[xColname, , drop = TRUE])),
  plotType = "bar",
  refLine = TRUE,
  refLineColor = "red",
  xlab = xColname,
  ylab = yColname,
  title,
  barColor = "dodgerblue4",
  barFill = "dodgerblue3",
  barSize = 0.1,
  barAlpha = 1,
  barWidth = 0.9,
  pointColor = "grey30",
  pointFill = "dodgerblue4",
  pointShape = 21,
  pointAlpha = 1,
  pointSize = 2,
  lineLayer = FALSE,
  lineColor = "dodgerblue4",
  lineSize = 1,
  lineType = "solid",
  lineFit = "loess",
  baseFontSize = 12,
  themeStyle = "grey",
  facet = TRUE,
  facetCol,
  xAngle = 45,
  scales = "free_y",
  debug = FALSE
)

Arguments

data	A tidy dataframe of data to plot (required) (see ?tidyContrasts).
facetColname	Define the column name to separate plots (required) (e.g. GeneID).
xColname	Define the column name to group boxplots by (required) (e.g. Contrast).
CI.R_colname	Define name of the CI high value (Default = "CI.R")
CI.L_colname	Define name of the CI low value (Default = "CI.L")
xOrder	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[xColname]))
plotType	one of "bar" or "point" (Default = bar")
refLine	Adds a horizontal line at y=0 (Default=TRUE)
refLineColor	Color for the reference line (Default="red")
xlab	X axis label (defaults to xColname)
ylab	Y axis label (defaults to yColname)
title	Plot title (optional)
barColor	Color for the bar outline (default = "dodgerblue4")
barFill	Color for the bar area (default = "dodgerblue3")
barSize	set the bar size (thickness of each bar perimeter; default = 0.1)
barAlpha	Transparency for the bar layer (Default = 1)
barWidth	set the bar width (Default = 0.8)
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)
lineLayer	Add a fitted line layer (Default = FALSE)
lineColor	Color of the line fit (Default = "dodgerblue4")
lineSize	Size of the line fit (Default = 1)
lineType	One of c("solid", "dashed", "dotted", "dotdash", "longdash", "twodash"). (Default = "solid")
lineFit	Type of fit to use. One of c("auto", "lm", "glm", "gam", "loess"). (Default = "loess")
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)
facetCol	Explicitly set the number of Rows for the facet plot. Default behavior will automatically set the columns. (Default = ceiling(sqrt(length(unique(data[facetCol])))))
xAngle	Angle to set the sample labels on the Xaxis (Default = 45; 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)
yColame	Define the column of values for plotting (Default = "logFC").
addLine	Adds a line if point layer chosen (Default = FALSE)

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

  #DGEobj example
  #Put contrasts in tidy format keeping logFC, and confidence limits data
  tidyDat <-tidyContrasts(dgeObj, rownameColumn="EnsgID", includeColumns = c("logFC", "CI.R", "CI.L"))

  #add gene symbols from geneData
  ens2genesym <- dgeObj$geneData %>%
                 rownames_to_column(var="EnsgID") %>%
                 select(EnsgID, GeneSymbol=GeneName)
  tidyDat <-  left_join(tidyDat, ens2genesym)

  #filter for a small set of genes of interest
  idx <- stringr::str_detect(tidyDat$GeneSymbol, "^PPAR")
  tidyDat <- tidyDat[idx,]

  #simple barplot
  logRatioPlot(tidyDat,
              facetColname = "GeneSymbol",
              xColname = "Contrast",
              facetCol = 2)

  #lineplot with some options
  logRatioPlot(tidyDat, plotType="point",
                     facetColname = "GeneSymbol",
                     xColname = "Contrast",
                     facetCol=4,
                     scales="fixed",
                     facet=TRUE,
                     title = "Test",
                     pointSize=4,
                     lineLayer=TRUE,
                     lineSize=0.1,
                     xAngle=60)

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