plot.gitter: Plot a gitter dat file

In gitter: Quantification of Pinned Microbial Cultures

Description

This function will plot a heatmap or bubble plot of a data.frame produced by gitter or a dat file saved to disk.

Usage

## S3 method for class 'gitter'
plot(x, title = "", type = "heatmap", low = "turquoise",
  mid = "black", high = "yellow", show.text = F, text.color = "white",
  norm = T, show.flags = T, flag.color = "white", ...)

Arguments

x	The data.frame produced by gitter or the path to a dat file saved by gitter.
title	Title of plot. Default is blank.
type	Type of plot. "heatmap" for a heatmap, "bubble" for a bubble plot. Default is "heatmap".
low	Color for the lower bound of colony sizes. Default is "turquoise".
mid	Color of the middle value of colony sizes. Default is "black".
high	Color for the upper bound of colony sizes. Default is "yellow".
show.text	Logical indicating if text representation of colony sizes should be overlaid on the plot. Default is TRUE.
text.color	Color of text if show.text is TRUE. Default is "white".
norm	Logical indicating if colony sizes should be normalized by dividing colony sizes the middle mean of values and capping them between 0-2. Default is TRUE.
show.flags	Logical indicating if dots should be overlaid on the plot for flagged colonies. Default is TRUE.
flag.color	Color of flag dot if show.flags is TRUE. Default is "white".
...	Additional arguments. Not used.

Value

a ggplot heatmap or bubble plot.

Examples

f = system.file("extdata", "sample.jpg.dat", package="gitter")
# Read in path as a gitter data object
g = gitter.read(f)
# Plot a heatmap
plot(g, type="heatmap")
# Show a bubble plot
plot(g, type="bubble", low="black", high="red")

Example output

xdpyinfo:  unable to open display "".
gitter version 1.1.1 - quantification of pinned microbial cultures

Copyright (C) 2015 Omar Wagih

Type 'gitter.demo()' for a demo, '?gitter' for help 
or see http://gitter.ccbr.utoronto.ca for more details
Warning message:
running command 'xdpyinfo  | grep 'dimensions:' 2>/dev/null' had status 1 
Warning message:
`axis.ticks.margin` is deprecated. Please set `margin` property  of `axis.text` instead 
Warning message:
`axis.ticks.margin` is deprecated. Please set `margin` property  of `axis.text` instead 

gitter documentation built on May 2, 2019, 9:14 a.m.