This function plots a matrix as a heatmap and saves it as a JPEG file.
Usage
create.heatmap(
matrix,
number.labels = FALSE,
title = NULL,
legend.label = "heatmap",
triangular = FALSE,
plot.dir = NULL,
fixed.scale = FALSE,
scale.min = NULL,
scale.max = NULL,
color.palette = "viridis",
show.legend = TRUE,
figure.width = 8,
figure.height = 6,
save = TRUE
)Arguments
- matrix
Matrix or dataframe containing spectral data.
- number.labels
Logical indicating whether to add number labels to the heatmap. Default is
FALSE.- title
Optional prefix for the plot filename. Default is
NULL, in which case the file will just be calledheatmap.jpg- legend.label
Character string that will appear on the heatmap legend. Default is
heatmap- triangular
Logical. Plot the lower triangle of the matrix only, diagonal included. Default is
FALSE.- plot.dir
Optional output directory. Default is
NULL, in which case the working directory will be used.- fixed.scale
Logical, determines whether to use an externally supplied fixed scale (min and max) for the heatmap color scale. Useful for putting multiple plots on the same scale. Default is
FALSE- scale.min
Optional numeric. Minimum for the fixed color scale. Default is
NULL, for no fixed scaling.- scale.max
Optional numeric. Maximum for the fixed color scale. Default is
NULL, for no fixed scaling.- color.palette
Optional character string defining the viridis color palette to be used for the fluorophore traces. Default is
viridis. Options are the viridis color options:magma,inferno,plasma,viridis,cividis,rocket,makoandturbo.- show.legend
Logical. If
TRUE, figure legend will be included.- figure.width
Numeric. Width of the heatmap figure. Default is
8.- figure.height
Numeric. Height of the heatmap figure. Default is
6.- save
Logical, if
TRUE, saves a JPEG file to theoutput.dir. Otherwise, the plot will simply be created in the Viewer.