Compute colors in classes distribution
colors.in.classes(
classes,
color1,
color2 = NULL,
mask = array(TRUE, dim(classes)),
N = max(classes, na.rm = TRUE),
type = "tresh",
thresh1 = NULL,
thresh2 = NULL,
sd1 = 2,
sd2 = 2,
col1 = "green",
col2 = "red",
test = FALSE,
plot = TRUE,
beside = TRUE,
ylim = NULL,
verbose = FALSE,
...
)Image of classes
Image of first color
Image of second color
Image mask
Maximum number of classes
Type of spot definition, see details
Threshold for first color image
Threshold for second color image
For automatic threshold, that is: mean(color1)+sd1*sd(color1)
For automatic threshold of color2
Name of color 1
Name of color 2
Compute tests: "Wilcoxon" for Wilcoxon rank-sum (Mann-Whitney U), chisq for Chi-squared test
Plot barplots
a logical value. If FALSE, the columns of height are portrayed as stacked bars, and if TRUE the columns are portrayed as juxtaposed bars.
limits for the y axis (plot)
verbose mode
additional plotting parameters
Table of classes with color 1 (and 2)
Type of spot definitions: "thresh" or "t": Threshold based (threshold can be given by thresh1/2 or automatically derived) "voxel" or "v": Spots are given as binary voxel mask "intensity" or "i": Voxels are weighted with voxel intensity. Intensity is scaled to [0,1] after subtracting thresh1/2 (or automatic threshold)