vsScatterPlot {vidger}R Documentation

Scatter plot of log_{10}(FPKM or CPM) values

Description

This function allows you to visualize comparisons of log_{10} values of either FPKM or CPM measurements of two treatments depending on analytical type.

Usage

vsScatterPlot(x, y, data, d.factor = NULL, type = c("cuffdiff", "deseq",
  "edger"), title = TRUE, grid = TRUE, highlight = NULL,
  data.return = FALSE, xaxis.text.size = 10, yaxis.text.size = 10,
  xaxis.title.size = 12, yaxis.title.size = 12, main.title.size = 15)

Arguments

x

treatment x for comparison (log_{2}(x/control)). This will be a factor level in your data.

y

treatment y for comparison (log_{2}(y/control)). This will be a factor level in your data.

data

output generated from calling the main routines of either cuffdiff, DESeq2, or edgeR analyses. For cuffdiff, this will be a *_exp.diff file. For DESeq2, this will be a generated object of class DESeqDataSet. For edgeR, this will be a generated object of class DGEList.

d.factor

a specified factor; for use with DESeq2 objects only. This input equates to the first parameter for the contrast argument when invoking the results() function in DESeq2. Defaults to NULL.

type

an analysis classifier to tell the function how to process the data. Must be either cuffdiff, deseq, or edger. cuffdiff must be used with cuffdiff data; deseq must be used for DESeq2 output; edgeR must be used with edgeR data. See the data parameter for further details.

title

display the main title of plot. Logical; defaults to TRUE. If set to FALSE, no title will display in plot.

grid

display major and minor axis lines. Logical; defaults to TRUE. If set to FALSE, no axis lines will display in plot.

highlight

character string of IDs that will be highlighted. Set to NULL if you do not want highlighted data.

data.return

returns data output of plot Logical; defaults to FALSE. If set to TRUE, a data frame will also be called. Assign to object for reproduction and saving of data frame. See final example for further details.

xaxis.text.size

change the font size of the x-axis text. Defaults to 10.

yaxis.text.size

change the font size of the y-axis text. Defaults to 10.

xaxis.title.size

change the font size of the x-axis title text. Defaults to 12.

yaxis.title.size

change the font size of the y-axis title text. Defaults to 12.

main.title.size

change the font size of the plot title text. Defaults to 15.

Value

An object created by ggplot

Author(s)

Brandon Monier, brandon.monier@sdstate.edu

Examples

# Cuffdiff example
data("df.cuff")
vsScatterPlot(
     x = "hESC", y = "iPS", data = df.cuff, d.factor = NULL,
     type = "cuffdiff", title = TRUE, grid = TRUE
)

# DESeq2 example
data("df.deseq")
require(DESeq2)
vsScatterPlot(
     x = "treated_paired.end", y = "untreated_paired.end",
     data = df.deseq, d.factor = "condition", type = "deseq",
     title = TRUE, grid = TRUE
)

# edgeR example
data("df.edger")
require(edgeR)
vsScatterPlot(
     x = "WW", y = "WM", data = df.edger, d.factor = NULL,
     type = "edger", title = TRUE, grid = TRUE
)

# Highlight IDs
data("df.cuff")
hl <- c(
     "XLOC_000033",
     "XLOC_000099",
     "XLOC_001414",
     "XLOC_001409"
)
vsScatterPlot(
     x = "hESC", y = "iPS", data = df.cuff, d.factor = NULL,
     type = "cuffdiff", title = TRUE, grid = TRUE, highlight = hl
)

# Extract data frame from visualization
data("df.cuff")
tmp <- vsScatterPlot(
     x = "hESC", y = "iPS", data = df.cuff, d.factor = NULL,
     type = "cuffdiff", title = TRUE, grid = TRUE, data.return = TRUE
)
df_scatter <- tmp[[1]] ## or use tmp$data
head(df_scatter)

# Show plot from object (see prior example for more details)
tmp[[2]] ## or use tmp$plot
[Package vidger version 1.2.1 Index]