image_plot_na: Wrapper for fields::image.plot function.

In rz6/CopulaHiC: Hi-C differential analysis via dependency modelling of chromatin interactions with generalized linear models

Description

Allows to mark -Inf, Inf and NA values in heatmaps with different colors. It will automatically detect such values and assign them color.

Usage

image_plot_na(
  z,
  breaks,
  col,
  na.color = "black",
  neg.inf.color = "gold",
  pos.inf.color = "darkgreen",
  ...
)

Arguments

z	numeric matrix to be plotted; may contain -Inf, Inf and NA values
breaks	numeric vector of breaks for colorscale
col	character vector of hex color strings; usually generated from some color pallette; it's length must be equal to length(breaks) - 1
na.color	color for NA values
neg.inf.color	color for -Inf values
pos.inf.color	color for Inf values
...	additional arguments passed to image.plot

See Also

image.plot for function which finally handles heatmap plotting

Examples

# matrix of data
mtx <- toeplitz(c(5:1))
# make lower triangle part negative
mtx[lower.tri(mtx)] <- -mtx[lower.tri(mtx)]
# make some cells -Inf
mtx[matrix(c(2,1,2,2,3,2), ncol = 2, byrow = TRUE)] <- -Inf
# make some cells Inf
mtx[matrix(c(3,5,4,5), ncol = 2, byrow = TRUE)] <- Inf
# make some cells NA
mtx[matrix(c(1,3,2,3,5,3), ncol = 2, byrow = TRUE)] <- NA
print(mtx)
# prepare breaks --> symmetric, from -5 to 5, spaced by 2, with 0 in the middle
# one can also introduce here log, sqrt or other scales by applying proper transformations
breaks <- sort(c(0,seq(-5,5,2)))
print(breaks)
# prepare symmetric color pallette indicating negtive values with blue, middle with white and positive with red
colors.pal = c("blue","white","red")
pal = colorRampPalette(colors.pal)
colors <- pal(length(breaks) - 1L)
# finally plot matrix
image_plot_na(mtx, breaks, colors)

rz6/CopulaHiC documentation built on Dec. 31, 2019, 9:19 a.m.