colors.in.classes {nucim} | R Documentation |
Compute colors in classes distribution
Description
Compute colors in classes distribution
Usage
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,
...
)
Arguments
classes |
Image of classes |
color1 |
Image of first color |
color2 |
Image of second color |
mask |
Image mask |
N |
Maximum number of classes |
type |
Type of spot definition, see details |
thresh1 |
Threshold for first color image |
thresh2 |
Threshold for second color image |
sd1 |
For automatic threshold, that is: mean(color1)+sd1*sd(color1) |
sd2 |
For automatic threshold of color2 |
col1 |
Name of color 1 |
col2 |
Name of color 2 |
test |
Compute tests: "Wilcoxon" for Wilcoxon rank-sum (Mann-Whitney U), chisq for Chi-squared test |
plot |
Plot barplots |
beside |
a logical value. If FALSE, the columns of height are portrayed as stacked bars, and if TRUE the columns are portrayed as juxtaposed bars. |
ylim |
limits for the y axis (plot) |
verbose |
verbose mode |
... |
additional plotting parameters |
Details
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)
Value
Table of classes with color 1 (and 2)