Plot correlation heatmaps
plot_correlation_heatmaps.Rd
Plot correlation heatmaps
Usage
plot_correlation_heatmaps(
e,
correlation_list_name,
channels = c("cfos", "eyfp", "colabel"),
colors = c("#be0000", "#00782e", "#f09b08"),
sig_color = "yellow",
sig_nudge_y = -0.7,
sig_size = 7,
ontology = "allen",
anatomical.order = c("Isocortex", "OLF", "HPF", "CTXsp", "CNU", "TH", "HY", "MB",
"HB", "CB"),
print_plot = TRUE,
save_plot = TRUE,
image_ext = ".png",
plot_title = NULL,
height = 10,
width = 10,
theme.hm = ggplot2::theme(axis.text.x = element_text(hjust = 1, vjust = 0.5, angle =
90, size = 8), axis.text.y = element_text(vjust = 0.5, size = 8), plot.title =
element_text(hjust = 0.5, size = 36), axis.title = element_text(size = 18),
legend.text = element_text(size = 22), legend.key.height = unit(100, "points"),
legend.title = element_text(size = 22), panel.spacing = unit(0.2, "lines"),
strip.text.x = element_text(angle = 0, hjust = 0.5, vjust = 0.5, size = 10),
strip.text.y = element_text(angle = 270, hjust = 0.5, vjust = 0.5, size = 10),
strip.placement = "outside", strip.background = element_rect(color = "black", fill =
"lightblue"))
)
Arguments
- e
experiment object. Must contain a named correlation_list object generated by
get_correlations()
- correlation_list_name
(str) The name of the correlation object generated by
get_correlations()
- channels
(str, default = c("cfos", "eyfp", "colabel")) Must exist in the channels attribute of the correlation_list.
- colors
(str, default = c("#be0000", "#00782e", "#f09b08")) Hexadecimal code for the colors corresponding channels parameter. Color values can also be input compatible with ggplot2 plotting functions.
- sig_color
(str, default = "yellow") Color of the significance symbol in R
- sig_nudge_y
(default = -0.7) Relative amount to nudge the significance symbols in the y direction to center over each square.
- sig_size
(default = 7) Point size for significance symbol.
- ontology
(str, default = "allen") Region ontology to use. options = "allen" or "unified"
- anatomical.order
(default = c("Isocortex", "OLF", "HPF", "CTXsp", "CNU","TH", "HY", "MB", "HB", "CB")) Default way to group subregions into super regions order
- print_plot
(bool, default = TRUE) Print the plot as graphics windows.
- save_plot
(bool, default = TRUE) Save into the figures subdirectory of the the experiment object output folder.
- image_ext
(default = ".png") image extension to the plot as.
- plot_title
(str, default = NULL) If NULL, the
correlation_list_name
will used as the title with underscores removed.- height
(int) Height of the plot in inches.
- width
(int) Width of the plot in inches.
- theme.hm
Option to use custom ggplot2 theme if the user wants. See default values as example.
Value
p_list A list the same length as the number of channels, with each element containing a plot handle for that channel.