R/themes.R
In nicohuttmann/pOmics: Framework for proteomics data analysis
Defines functions
theme_epitope_peptides_plot
theme_thesis_cor_matrix
theme_thesis_framed_no_axis
theme_phosprot_half_open
theme_iDC_heatmap_w_legend
theme_iDC_heatmap_labels_y
theme_iDC_heatmap_labels_x
theme_iDC_annot_layer
theme_iDC_dendrogram
theme_hjv_overlap_heatmap
theme_hjv_heatmap_only_noframe
theme_hjv_heatmap_only
theme_hjv_heatmap
theme_hjv_half_open
theme_hjv_framed_no_axes
theme_hjv_framed
Documented in
theme_epitope_peptides_plot
theme_hjv_framed
theme_hjv_framed_no_axes
theme_hjv_half_open
theme_hjv_heatmap
theme_hjv_heatmap_only
theme_hjv_heatmap_only_noframe
theme_hjv_overlap_heatmap
theme_iDC_annot_layer
theme_iDC_dendrogram
theme_iDC_heatmap_labels_x
theme_iDC_heatmap_labels_y
theme_iDC_heatmap_w_legend
theme_phosprot_half_open
theme_thesis_cor_matrix
theme_thesis_framed_no_axis
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_hjv_framed <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(color = "black", size = small_size),
axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
axis.text.y = element_text(margin = margin(r = small_size / 4), hjust = 1),
axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_line(color = "black", size = line_size),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title.x = element_text(
margin = margin(t = half_line / 2),
vjust = 1
),
axis.title.x.top = element_text(
margin = margin(b = half_line / 2),
vjust = 0
),
axis.title.y = element_text(
angle = 90,
margin = margin(r = half_line / 2),
vjust = 1
),
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
vjust = 0
),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_rect(color = "black", size = line_size_orig),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = margin(half_line, half_line, half_line, half_line),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_hjv_framed_no_axes <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_blank(),
axis.text.x = NULL,
axis.text.x.top = NULL,
axis.text.y = NULL,
axis.text.y.right = NULL,
axis.ticks = element_blank(),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title.x = element_text(
margin = margin(t = half_line / 2),
vjust = 1
),
axis.title.x.top = element_text(
margin = margin(b = half_line / 2),
vjust = 0
),
axis.title.y = element_text(
angle = 90,
margin = margin(r = half_line / 2),
vjust = 1
),
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
vjust = 0
),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_rect(color = "black", size = line_size_orig),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = margin(half_line, half_line, half_line, half_line),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_hjv_half_open <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(color = "black", size = small_size),
axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
axis.text.y = element_text(margin = margin(r = small_size / 4), hjust = 1),
axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_line(color = "black", size = line_size),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title.x = element_text(
margin = margin(t = half_line / 2),
vjust = 1
),
axis.title.x.top = element_text(
margin = margin(b = half_line / 2),
vjust = 0
),
axis.title.y = element_text(
angle = 90,
margin = margin(r = half_line / 2),
vjust = 1
),
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
vjust = 0
),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = margin(half_line, half_line, half_line, half_line),
complete = TRUE
)
}
#' Create a theme for heatmaps for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#' @return The theme.
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_hjv_heatmap <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(color = "black", size = small_size),
axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
axis.text.x.top = NULL,
axis.text.y = element_text(margin = margin(r = small_size / 4), hjust = 1),
axis.text.y.right = NULL,
axis.ticks = element_blank(),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title.x = element_text(
margin = margin(t = half_line / 2),
vjust = 1
),
axis.title.x.top = element_text(
margin = margin(b = half_line / 2),
vjust = 0
),
axis.title.y = element_text(
angle = 90,
margin = margin(r = half_line / 2),
vjust = 1
),
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
vjust = 0
),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_rect(color = "black", size = line_size_orig),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = margin(half_line, half_line, half_line, half_line),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_hjv_heatmap_only <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(),
# axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
# axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
axis.text.y = element_blank(), element_text(margin = margin(r = small_size / 4), hjust = 1),
# axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title = element_blank(),
# axis.title.x = element_text(
# margin = margin(t = half_line / 2),
# vjust = 1
# ),
# axis.title.x.top = element_text(
# margin = margin(b = half_line / 2),
# vjust = 0
# ),
# axis.title.y = element_text(
# angle = 90,
# margin = margin(r = half_line / 2),
# vjust = 1
# ),
# axis.title.y.right = element_text(
# angle = -90,
# margin = margin(l = half_line / 2),
# vjust = 0
# ),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "none",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_rect(color = "black", size = line_size_orig),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = unit(c(0, 0, 0, 0), "null"),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_hjv_heatmap_only_noframe <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(),
# axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
# axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
axis.text.y = element_blank(), element_text(margin = margin(r = small_size / 4), hjust = 1),
# axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title = element_blank(),
# axis.title.x = element_text(
# margin = margin(t = half_line / 2),
# vjust = 1
# ),
# axis.title.x.top = element_text(
# margin = margin(b = half_line / 2),
# vjust = 0
# ),
# axis.title.y = element_text(
# angle = 90,
# margin = margin(r = half_line / 2),
# vjust = 1
# ),
# axis.title.y.right = element_text(
# angle = -90,
# margin = margin(l = half_line / 2),
# vjust = 0
# ),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "none",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = unit(c(0, 0, 0, 0), "null"),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_hjv_overlap_heatmap <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(color = "black", size = small_size),
axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
axis.text.y = element_text(margin = margin(r = small_size / 4), hjust = 1),
axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title.x = element_text(
margin = margin(t = half_line / 2),
vjust = 1
),
axis.title.x.top = element_text(
margin = margin(b = half_line / 2),
vjust = 0
),
axis.title.y = element_text(
angle = 90,
margin = margin(r = half_line / 2),
vjust = 1
),
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
vjust = 0
),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_rect(color = "black", size = line_size_orig),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = margin(half_line, half_line, half_line, half_line),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_iDC_dendrogram <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_blank(),
# axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
# axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
#axis.text.y = element_blank(), element_text(margin = margin(r = small_size / 4), hjust = 1),
# axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(0, "pt"),
axis.title = element_blank(),
# axis.title.x = element_text(
# margin = margin(t = half_line / 2),
# vjust = 1
# ),
# axis.title.x.top = element_text(
# margin = margin(b = half_line / 2),
# vjust = 0
# ),
# axis.title.y = element_text(
# angle = 90,
# margin = margin(r = half_line / 2),
# vjust = 1
# ),
# axis.title.y.right = element_text(
# angle = -90,
# margin = margin(l = half_line / 2),
# vjust = 0
# ),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "none",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = unit(c(0, 0, 0, 0), "null"),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_iDC_annot_layer <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_blank(),
# axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
# axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
axis.text.y = element_blank(),
# axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(0, "pt"),
axis.title = element_blank(),
# axis.title.x = element_text(
# margin = margin(t = half_line / 2),
# vjust = 1
# ),
# axis.title.x.top = element_text(
# margin = margin(b = half_line / 2),
# vjust = 0
# ),
# axis.title.y = element_text(
# angle = 90,
# margin = margin(r = half_line / 2),
# vjust = 1
# ),
# axis.title.y.right = element_text(
# angle = -90,
# margin = margin(l = half_line / 2),
# vjust = 0
# ),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = unit(c(0, 0, 0, 0), "null"),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_iDC_heatmap_labels_x <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(color = "black", size = small_size),
axis.text.x = element_text(hjust = 1, angle = 45),
#axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
axis.text.y = element_blank(),
#axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(0, "pt"),
axis.title = element_blank(),
# axis.title.x.top = element_text(
# margin = margin(b = half_line / 2),
# vjust = 0
# ),
# axis.title.y = element_text(
# angle = 90,
# margin = margin(r = half_line / 2),
# vjust = 1
# ),
# axis.title.y.right = element_text(
# angle = -90,
# margin = margin(l = half_line / 2),
# vjust = 0
# ),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_blank(),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = unit(c(0, 0, 0, 0), "cm"),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_iDC_heatmap_labels_y <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(color = "black", size = small_size),
axis.text.x = element_blank(),
#axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
axis.text.y = element_text(hjust = 0),
#axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(0, "pt"),
axis.title = element_blank(),
# axis.title.x.top = element_text(
# margin = margin(b = half_line / 2),
# vjust = 0
# ),
# axis.title.y = element_text(
# angle = 90,
# margin = margin(r = half_line / 2),
# vjust = 1
# ),
# axis.title.y.right = element_text(
# angle = -90,
# margin = margin(l = half_line / 2),
# vjust = 0
# ),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_blank(),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = unit(c(0, 0, 0, 0), "cm"),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_iDC_heatmap_w_legend <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_blank(),
# axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
# axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
#axis.text.y = element_blank(),
# axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(0, "pt"),
axis.title = element_blank(),
# axis.title.x = element_text(
# margin = margin(t = half_line / 2),
# vjust = 1
# ),
# axis.title.x.top = element_text(
# margin = margin(b = half_line / 2),
# vjust = 0
# ),
# axis.title.y = element_text(
# angle = 90,
# margin = margin(r = half_line / 2),
# vjust = 1
# ),
# axis.title.y.right = element_text(
# angle = -90,
# margin = margin(l = half_line / 2),
# vjust = 0
# ),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_rect(color = "black", size = line_size_orig),
panel.grid = element_blank(),
# panel.grid.major = NULL,
# panel.grid.minor = NULL,
# panel.grid.major.x = NULL,
# panel.grid.major.y = NULL,
# panel.grid.minor.x = NULL,
# panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = unit(c(0, 0, 0, 0), "null"),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_size_small Relative size of small text (e.g., axis tick labels)
#' @param font_size_tiny Relative size of tiny text (e.g., caption)
#' @param font_size_large Relative size of large text (e.g., title)
#' @param font_family Font family for plot title, axis titles and labels,
#' legend texts, etc.
#' @param line_size Line size for axis lines.
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_phosprot_half_open <- function(font_size = 8,
font_size_small = 7,
font_size_tiny = 6,
font_size_large = 10,
font_family = "",
line_size = .5) {
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black",
size = line_size,
linetype = 1,
lineend = "butt"),
rect = element_rect(fill = NA, color = NA,
size = line_size,
linetype = 1),
text = element_text(family = font_family,
face = "plain",
color = "black",
size = font_size,
hjust = 0.5,
vjust = 0.5,
angle = 0,
lineheight = .9,
margin = margin(),
debug = FALSE),
axis.line = element_line(color = "black",
size = line_size,
lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(color = "black", size = font_size_small),
axis.text.x = element_text(margin = margin(t = font_size_small / 4),
vjust = 1),
axis.text.x.top = element_text(margin = margin(b = font_size_small / 4),
vjust = 0),
axis.text.y = element_text(margin = margin(r = font_size_small / 4),
hjust = 1),
axis.text.y.right = element_text(margin = margin(l = font_size_small / 4),
hjust = 0),
axis.ticks = element_line(color = "black", size = line_size),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title.x = element_text(
margin = margin(t = half_line / 2),
vjust = 1
),
axis.title.x.top = element_text(
margin = margin(b = half_line / 2),
vjust = 0
),
axis.title.y = element_text(
angle = 90,
margin = margin(r = half_line / 2),
vjust = 1
),
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
vjust = 0
),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = font_size_small),
legend.text.align = NULL,
legend.title = element_text(hjust = 0, size = font_size_small),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = font_size_small,
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = font_size_large,
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = font_size_small,
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = font_size_tiny,
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = margin(half_line, half_line, half_line, half_line),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_size_small Relative size of small text (e.g., axis tick labels)
#' @param font_size_tiny Relative size of tiny text (e.g., caption)
#' @param font_size_large Relative size of large text (e.g., title)
#' @param font_family Font family for plot title, axis titles and labels,
#' legend texts, etc.
#' @param line_size Line size for axis lines.
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_thesis_framed_no_axis <- function(font_size = 8,
font_size_small = 7,
font_size_tiny = 6,
font_size_large = 10,
font_family = "",
line_size = .5) {
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black",
size = line_size,
linetype = 1,
lineend = "butt"),
rect = element_rect(fill = NA, color = NA,
size = line_size,
linetype = 1),
text = element_text(family = font_family,
face = "plain",
color = "black",
size = font_size,
hjust = 0.5,
vjust = 0.5,
angle = 0,
lineheight = .9,
margin = margin(),
debug = FALSE),
axis.line = element_blank(),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_blank(),
axis.text.x = NULL,
axis.text.x.top = NULL,
axis.text.y = NULL,
axis.text.y.right = NULL,
axis.ticks = element_blank(),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title.x = element_text(
margin = margin(t = half_line / 2),
vjust = 1
),
axis.title.x.top = element_text(
margin = margin(b = half_line / 2),
vjust = 0
),
axis.title.y = element_text(
angle = 90,
margin = margin(r = half_line / 2),
vjust = 1
),
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
vjust = 0
),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = font_size),
legend.text.align = NULL,
legend.title = element_text(hjust = 0, size = font_size),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_rect(color = "black", size = line_size),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = font_size_small,
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = font_size_large,
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = font_size_small,
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = font_size_tiny,
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = margin(half_line, half_line, half_line, half_line),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_thesis_cor_matrix <- function(font_size = 8,
font_family = "",
line_size = .5,
rel_small = 12/14,
rel_tiny = 11/14,
rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_blank(),
# axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
# axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
#axis.text.y = element_blank(),
# axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(0, "pt"),
axis.title = element_blank(),
# axis.title.x = element_text(
# margin = margin(t = half_line / 2),
# vjust = 1
# ),
# axis.title.x.top = element_text(
# margin = margin(b = half_line / 2),
# vjust = 0
# ),
# axis.title.y = element_text(
# angle = 90,
# margin = margin(r = half_line / 2),
# vjust = 1
# ),
# axis.title.y.right = element_text(
# angle = -90,
# margin = margin(l = half_line / 2),
# vjust = 0
# ),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "none",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_rect(color = "black", size = line_size_orig),
panel.grid = element_blank(),
# panel.grid.major = NULL,
# panel.grid.minor = NULL,
# panel.grid.major.x = NULL,
# panel.grid.major.y = NULL,
# panel.grid.minor.x = NULL,
# panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = unit(c(0, 0, 0, 0), "null"),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_size_small Relative size of small text (e.g., axis tick labels)
#' @param font_size_tiny Relative size of tiny text (e.g., caption)
#' @param font_size_large Relative size of large text (e.g., title)
#' @param font_family Font family for plot title, axis titles and labels,
#' legend texts, etc.
#' @param line_size Line size for axis lines.
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_epitope_peptides_plot <- function(font_size = 8,
font_size_small = 7,
font_size_tiny = 6,
font_size_large = 10,
font_family = "",
line_size = .5) {
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black",
size = line_size,
linetype = 1,
lineend = "butt"),
rect = element_rect(fill = NA, color = NA,
size = line_size,
linetype = 1),
text = element_text(family = font_family,
face = "plain",
color = "black",
size = font_size,
hjust = 0.5,
vjust = 0.5,
angle = 0,
lineheight = .9,
margin = margin(),
debug = FALSE),
axis.line = element_line(color = "black",
size = line_size,
lineend = "square"),
axis.line.x = element_blank(),
axis.line.y = NULL,
axis.text = element_text(color = "black", size = font_size_small),
axis.text.x = element_text(margin = margin(t = font_size_small / 4),
vjust = 1),
axis.text.x.top = element_text(margin = margin(b = font_size_small / 4),
vjust = 0),
axis.text.y = element_text(margin = margin(r = font_size_small / 4),
hjust = 1),
axis.text.y.right = element_text(margin = margin(l = font_size_small / 4),
hjust = 0),
axis.ticks = element_line(color = "black", size = line_size),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title.x = element_text(
margin = margin(t = half_line / 2),
vjust = 1
),
axis.title.x.top = element_text(
margin = margin(b = half_line / 2),
vjust = 0
),
axis.title.y = element_text(
angle = 90,
margin = margin(r = half_line / 2),
vjust = 1
),
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
vjust = 0
),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = font_size_small),
legend.text.align = NULL,
legend.title = element_text(hjust = 0, size = font_size_small),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = font_size_small,
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = font_size_large,
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = font_size_small,
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = font_size_tiny,
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = margin(half_line, half_line, half_line, half_line),
complete = TRUE
)
}
nicohuttmann/pOmics documentation built on Sept. 21, 2022, 9:28 a.m.
R Package Documentation
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Defines functions theme_epitope_peptides_plot theme_thesis_cor_matrix theme_thesis_framed_no_axis theme_phosprot_half_open theme_iDC_heatmap_w_legend theme_iDC_heatmap_labels_y theme_iDC_heatmap_labels_x theme_iDC_annot_layer theme_iDC_dendrogram theme_hjv_overlap_heatmap theme_hjv_heatmap_only_noframe theme_hjv_heatmap_only theme_hjv_heatmap theme_hjv_half_open theme_hjv_framed_no_axes theme_hjv_framed
Documented in theme_epitope_peptides_plot theme_hjv_framed theme_hjv_framed_no_axes theme_hjv_half_open theme_hjv_heatmap theme_hjv_heatmap_only theme_hjv_heatmap_only_noframe theme_hjv_overlap_heatmap theme_iDC_annot_layer theme_iDC_dendrogram theme_iDC_heatmap_labels_x theme_iDC_heatmap_labels_y theme_iDC_heatmap_w_legend theme_phosprot_half_open theme_thesis_cor_matrix theme_thesis_framed_no_axis
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_hjv_framed <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(color = "black", size = small_size),
axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
axis.text.y = element_text(margin = margin(r = small_size / 4), hjust = 1),
axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_line(color = "black", size = line_size),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title.x = element_text(
margin = margin(t = half_line / 2),
vjust = 1
),
axis.title.x.top = element_text(
margin = margin(b = half_line / 2),
vjust = 0
),
axis.title.y = element_text(
angle = 90,
margin = margin(r = half_line / 2),
vjust = 1
),
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
vjust = 0
),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_rect(color = "black", size = line_size_orig),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = margin(half_line, half_line, half_line, half_line),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_hjv_framed_no_axes <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_blank(),
axis.text.x = NULL,
axis.text.x.top = NULL,
axis.text.y = NULL,
axis.text.y.right = NULL,
axis.ticks = element_blank(),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title.x = element_text(
margin = margin(t = half_line / 2),
vjust = 1
),
axis.title.x.top = element_text(
margin = margin(b = half_line / 2),
vjust = 0
),
axis.title.y = element_text(
angle = 90,
margin = margin(r = half_line / 2),
vjust = 1
),
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
vjust = 0
),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_rect(color = "black", size = line_size_orig),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = margin(half_line, half_line, half_line, half_line),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_hjv_half_open <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(color = "black", size = small_size),
axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
axis.text.y = element_text(margin = margin(r = small_size / 4), hjust = 1),
axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_line(color = "black", size = line_size),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title.x = element_text(
margin = margin(t = half_line / 2),
vjust = 1
),
axis.title.x.top = element_text(
margin = margin(b = half_line / 2),
vjust = 0
),
axis.title.y = element_text(
angle = 90,
margin = margin(r = half_line / 2),
vjust = 1
),
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
vjust = 0
),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = margin(half_line, half_line, half_line, half_line),
complete = TRUE
)
}
#' Create a theme for heatmaps for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#' @return The theme.
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_hjv_heatmap <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(color = "black", size = small_size),
axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
axis.text.x.top = NULL,
axis.text.y = element_text(margin = margin(r = small_size / 4), hjust = 1),
axis.text.y.right = NULL,
axis.ticks = element_blank(),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title.x = element_text(
margin = margin(t = half_line / 2),
vjust = 1
),
axis.title.x.top = element_text(
margin = margin(b = half_line / 2),
vjust = 0
),
axis.title.y = element_text(
angle = 90,
margin = margin(r = half_line / 2),
vjust = 1
),
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
vjust = 0
),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_rect(color = "black", size = line_size_orig),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = margin(half_line, half_line, half_line, half_line),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_hjv_heatmap_only <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(),
# axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
# axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
axis.text.y = element_blank(), element_text(margin = margin(r = small_size / 4), hjust = 1),
# axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title = element_blank(),
# axis.title.x = element_text(
# margin = margin(t = half_line / 2),
# vjust = 1
# ),
# axis.title.x.top = element_text(
# margin = margin(b = half_line / 2),
# vjust = 0
# ),
# axis.title.y = element_text(
# angle = 90,
# margin = margin(r = half_line / 2),
# vjust = 1
# ),
# axis.title.y.right = element_text(
# angle = -90,
# margin = margin(l = half_line / 2),
# vjust = 0
# ),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "none",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_rect(color = "black", size = line_size_orig),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = unit(c(0, 0, 0, 0), "null"),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_hjv_heatmap_only_noframe <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(),
# axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
# axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
axis.text.y = element_blank(), element_text(margin = margin(r = small_size / 4), hjust = 1),
# axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title = element_blank(),
# axis.title.x = element_text(
# margin = margin(t = half_line / 2),
# vjust = 1
# ),
# axis.title.x.top = element_text(
# margin = margin(b = half_line / 2),
# vjust = 0
# ),
# axis.title.y = element_text(
# angle = 90,
# margin = margin(r = half_line / 2),
# vjust = 1
# ),
# axis.title.y.right = element_text(
# angle = -90,
# margin = margin(l = half_line / 2),
# vjust = 0
# ),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "none",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = unit(c(0, 0, 0, 0), "null"),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_hjv_overlap_heatmap <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(color = "black", size = small_size),
axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
axis.text.y = element_text(margin = margin(r = small_size / 4), hjust = 1),
axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title.x = element_text(
margin = margin(t = half_line / 2),
vjust = 1
),
axis.title.x.top = element_text(
margin = margin(b = half_line / 2),
vjust = 0
),
axis.title.y = element_text(
angle = 90,
margin = margin(r = half_line / 2),
vjust = 1
),
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
vjust = 0
),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_rect(color = "black", size = line_size_orig),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = margin(half_line, half_line, half_line, half_line),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_iDC_dendrogram <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_blank(),
# axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
# axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
#axis.text.y = element_blank(), element_text(margin = margin(r = small_size / 4), hjust = 1),
# axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(0, "pt"),
axis.title = element_blank(),
# axis.title.x = element_text(
# margin = margin(t = half_line / 2),
# vjust = 1
# ),
# axis.title.x.top = element_text(
# margin = margin(b = half_line / 2),
# vjust = 0
# ),
# axis.title.y = element_text(
# angle = 90,
# margin = margin(r = half_line / 2),
# vjust = 1
# ),
# axis.title.y.right = element_text(
# angle = -90,
# margin = margin(l = half_line / 2),
# vjust = 0
# ),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "none",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = unit(c(0, 0, 0, 0), "null"),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_iDC_annot_layer <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_blank(),
# axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
# axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
axis.text.y = element_blank(),
# axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(0, "pt"),
axis.title = element_blank(),
# axis.title.x = element_text(
# margin = margin(t = half_line / 2),
# vjust = 1
# ),
# axis.title.x.top = element_text(
# margin = margin(b = half_line / 2),
# vjust = 0
# ),
# axis.title.y = element_text(
# angle = 90,
# margin = margin(r = half_line / 2),
# vjust = 1
# ),
# axis.title.y.right = element_text(
# angle = -90,
# margin = margin(l = half_line / 2),
# vjust = 0
# ),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = unit(c(0, 0, 0, 0), "null"),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_iDC_heatmap_labels_x <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(color = "black", size = small_size),
axis.text.x = element_text(hjust = 1, angle = 45),
#axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
axis.text.y = element_blank(),
#axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(0, "pt"),
axis.title = element_blank(),
# axis.title.x.top = element_text(
# margin = margin(b = half_line / 2),
# vjust = 0
# ),
# axis.title.y = element_text(
# angle = 90,
# margin = margin(r = half_line / 2),
# vjust = 1
# ),
# axis.title.y.right = element_text(
# angle = -90,
# margin = margin(l = half_line / 2),
# vjust = 0
# ),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_blank(),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = unit(c(0, 0, 0, 0), "cm"),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_iDC_heatmap_labels_y <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(color = "black", size = small_size),
axis.text.x = element_blank(),
#axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
axis.text.y = element_text(hjust = 0),
#axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(0, "pt"),
axis.title = element_blank(),
# axis.title.x.top = element_text(
# margin = margin(b = half_line / 2),
# vjust = 0
# ),
# axis.title.y = element_text(
# angle = 90,
# margin = margin(r = half_line / 2),
# vjust = 1
# ),
# axis.title.y.right = element_text(
# angle = -90,
# margin = margin(l = half_line / 2),
# vjust = 0
# ),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_blank(),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = unit(c(0, 0, 0, 0), "cm"),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_iDC_heatmap_w_legend <- function(font_size = 8, font_family = "", line_size = .5,
rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_blank(),
# axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
# axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
#axis.text.y = element_blank(),
# axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(0, "pt"),
axis.title = element_blank(),
# axis.title.x = element_text(
# margin = margin(t = half_line / 2),
# vjust = 1
# ),
# axis.title.x.top = element_text(
# margin = margin(b = half_line / 2),
# vjust = 0
# ),
# axis.title.y = element_text(
# angle = 90,
# margin = margin(r = half_line / 2),
# vjust = 1
# ),
# axis.title.y.right = element_text(
# angle = -90,
# margin = margin(l = half_line / 2),
# vjust = 0
# ),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_rect(color = "black", size = line_size_orig),
panel.grid = element_blank(),
# panel.grid.major = NULL,
# panel.grid.minor = NULL,
# panel.grid.major.x = NULL,
# panel.grid.major.y = NULL,
# panel.grid.minor.x = NULL,
# panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = unit(c(0, 0, 0, 0), "null"),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_size_small Relative size of small text (e.g., axis tick labels)
#' @param font_size_tiny Relative size of tiny text (e.g., caption)
#' @param font_size_large Relative size of large text (e.g., title)
#' @param font_family Font family for plot title, axis titles and labels,
#' legend texts, etc.
#' @param line_size Line size for axis lines.
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_phosprot_half_open <- function(font_size = 8,
font_size_small = 7,
font_size_tiny = 6,
font_size_large = 10,
font_family = "",
line_size = .5) {
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black",
size = line_size,
linetype = 1,
lineend = "butt"),
rect = element_rect(fill = NA, color = NA,
size = line_size,
linetype = 1),
text = element_text(family = font_family,
face = "plain",
color = "black",
size = font_size,
hjust = 0.5,
vjust = 0.5,
angle = 0,
lineheight = .9,
margin = margin(),
debug = FALSE),
axis.line = element_line(color = "black",
size = line_size,
lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(color = "black", size = font_size_small),
axis.text.x = element_text(margin = margin(t = font_size_small / 4),
vjust = 1),
axis.text.x.top = element_text(margin = margin(b = font_size_small / 4),
vjust = 0),
axis.text.y = element_text(margin = margin(r = font_size_small / 4),
hjust = 1),
axis.text.y.right = element_text(margin = margin(l = font_size_small / 4),
hjust = 0),
axis.ticks = element_line(color = "black", size = line_size),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title.x = element_text(
margin = margin(t = half_line / 2),
vjust = 1
),
axis.title.x.top = element_text(
margin = margin(b = half_line / 2),
vjust = 0
),
axis.title.y = element_text(
angle = 90,
margin = margin(r = half_line / 2),
vjust = 1
),
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
vjust = 0
),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = font_size_small),
legend.text.align = NULL,
legend.title = element_text(hjust = 0, size = font_size_small),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = font_size_small,
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = font_size_large,
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = font_size_small,
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = font_size_tiny,
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = margin(half_line, half_line, half_line, half_line),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_size_small Relative size of small text (e.g., axis tick labels)
#' @param font_size_tiny Relative size of tiny text (e.g., caption)
#' @param font_size_large Relative size of large text (e.g., title)
#' @param font_family Font family for plot title, axis titles and labels,
#' legend texts, etc.
#' @param line_size Line size for axis lines.
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_thesis_framed_no_axis <- function(font_size = 8,
font_size_small = 7,
font_size_tiny = 6,
font_size_large = 10,
font_family = "",
line_size = .5) {
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black",
size = line_size,
linetype = 1,
lineend = "butt"),
rect = element_rect(fill = NA, color = NA,
size = line_size,
linetype = 1),
text = element_text(family = font_family,
face = "plain",
color = "black",
size = font_size,
hjust = 0.5,
vjust = 0.5,
angle = 0,
lineheight = .9,
margin = margin(),
debug = FALSE),
axis.line = element_blank(),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_blank(),
axis.text.x = NULL,
axis.text.x.top = NULL,
axis.text.y = NULL,
axis.text.y.right = NULL,
axis.ticks = element_blank(),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title.x = element_text(
margin = margin(t = half_line / 2),
vjust = 1
),
axis.title.x.top = element_text(
margin = margin(b = half_line / 2),
vjust = 0
),
axis.title.y = element_text(
angle = 90,
margin = margin(r = half_line / 2),
vjust = 1
),
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
vjust = 0
),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = font_size),
legend.text.align = NULL,
legend.title = element_text(hjust = 0, size = font_size),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_rect(color = "black", size = line_size),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = font_size_small,
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = font_size_large,
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = font_size_small,
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = font_size_tiny,
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = margin(half_line, half_line, half_line, half_line),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_family Font family for plot title, axis titles and labels, legend texts, etc.
#' @param line_size Line size for axis lines.
#' @param rel_small Relative size of small text (e.g., axis tick labels)
#' @param rel_tiny Relative size of tiny text (e.g., caption)
#' @param rel_large Relative size of large text (e.g., title)
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_thesis_cor_matrix <- function(font_size = 8,
font_family = "",
line_size = .5,
rel_small = 12/14,
rel_tiny = 11/14,
rel_large = 16/14) {
line_size_orig <- line_size
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
small_size <- rel_small * font_size
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black", size = line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = NA, color = NA, size = line_size, linetype = 1),
text = element_text(family = font_family, face = "plain", color = "black",
size = font_size, hjust = 0.5, vjust = 0.5, angle = 0, lineheight = .9,
margin = margin(), debug = FALSE),
axis.line = element_blank(), #element_line(color = "black", size = line_size, lineend = "square"),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_blank(),
# axis.text.x = element_text(margin = margin(t = small_size / 4), vjust = 1),
# axis.text.x.top = element_text(margin = margin(b = small_size / 4), vjust = 0),
#axis.text.y = element_blank(),
# axis.text.y.right = element_text(margin = margin(l = small_size / 4), hjust = 0),
axis.ticks = element_blank(),
axis.ticks.length = unit(0, "pt"),
axis.title = element_blank(),
# axis.title.x = element_text(
# margin = margin(t = half_line / 2),
# vjust = 1
# ),
# axis.title.x.top = element_text(
# margin = margin(b = half_line / 2),
# vjust = 0
# ),
# axis.title.y = element_text(
# angle = 90,
# margin = margin(r = half_line / 2),
# vjust = 1
# ),
# axis.title.y.right = element_text(
# angle = -90,
# margin = margin(l = half_line / 2),
# vjust = 0
# ),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(rel_small)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "none",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_rect(color = "black", size = line_size_orig),
panel.grid = element_blank(),
# panel.grid.major = NULL,
# panel.grid.minor = NULL,
# panel.grid.major.x = NULL,
# panel.grid.major.y = NULL,
# panel.grid.minor.x = NULL,
# panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = rel(rel_small),
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = rel(rel_large),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = rel(rel_small),
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = rel(rel_tiny),
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = unit(c(0, 0, 0, 0), "null"),
complete = TRUE
)
}
#' Create a theme for half open plots for Hjv project
#'
#'
#' @param font_size Overall font size.
#' @param font_size_small Relative size of small text (e.g., axis tick labels)
#' @param font_size_tiny Relative size of tiny text (e.g., caption)
#' @param font_size_large Relative size of large text (e.g., title)
#' @param font_family Font family for plot title, axis titles and labels,
#' legend texts, etc.
#' @param line_size Line size for axis lines.
#'
#' @return The theme.
#' @export
#'
#' @importFrom ggplot2 margin theme_grey theme %+replace%
#' @importFrom grid unit
#'
theme_epitope_peptides_plot <- function(font_size = 8,
font_size_small = 7,
font_size_tiny = 6,
font_size_large = 10,
font_family = "",
line_size = .5) {
line_size <- line_size / (ggplot2::.pt * 72.27 / 96)
half_line <- font_size / 2
# work off of theme_grey just in case some new theme element comes along
theme_grey(base_size = font_size, base_family = font_family) %+replace%
theme(
line = element_line(color = "black",
size = line_size,
linetype = 1,
lineend = "butt"),
rect = element_rect(fill = NA, color = NA,
size = line_size,
linetype = 1),
text = element_text(family = font_family,
face = "plain",
color = "black",
size = font_size,
hjust = 0.5,
vjust = 0.5,
angle = 0,
lineheight = .9,
margin = margin(),
debug = FALSE),
axis.line = element_line(color = "black",
size = line_size,
lineend = "square"),
axis.line.x = element_blank(),
axis.line.y = NULL,
axis.text = element_text(color = "black", size = font_size_small),
axis.text.x = element_text(margin = margin(t = font_size_small / 4),
vjust = 1),
axis.text.x.top = element_text(margin = margin(b = font_size_small / 4),
vjust = 0),
axis.text.y = element_text(margin = margin(r = font_size_small / 4),
hjust = 1),
axis.text.y.right = element_text(margin = margin(l = font_size_small / 4),
hjust = 0),
axis.ticks = element_line(color = "black", size = line_size),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.title.x = element_text(
margin = margin(t = half_line / 2),
vjust = 1
),
axis.title.x.top = element_text(
margin = margin(b = half_line / 2),
vjust = 0
),
axis.title.y = element_text(
angle = 90,
margin = margin(r = half_line / 2),
vjust = 1
),
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
vjust = 0
),
legend.background = element_blank(),
legend.spacing = unit(font_size, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(0, 0, 0, 0),
legend.key = element_blank(),
legend.key.size = unit(1.1 * font_size, "pt"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = font_size_small),
legend.text.align = NULL,
legend.title = element_text(hjust = 0, size = font_size_small),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = c("left", "center"),
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0),
legend.box.background = element_blank(),
legend.box.spacing = unit(font_size, "pt"),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid = element_blank(),
panel.grid.major = NULL,
panel.grid.minor = NULL,
panel.grid.major.x = NULL,
panel.grid.major.y = NULL,
panel.grid.minor.x = NULL,
panel.grid.minor.y = NULL,
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey80"),
strip.text = element_text(
size = font_size_small,
margin = margin(half_line / 2, half_line / 2,
half_line / 2, half_line / 2)
),
strip.text.x = NULL,
strip.text.y = element_text(angle = -90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line / 2, "pt"),
strip.switch.pad.wrap = unit(half_line / 2, "pt"),
plot.background = element_blank(),
plot.title = element_text(
face = "bold",
size = font_size_large,
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.subtitle = element_text(
size = font_size_small,
hjust = 0, vjust = 1,
margin = margin(b = half_line)
),
plot.caption = element_text(
size = font_size_tiny,
hjust = 1, vjust = 1,
margin = margin(t = half_line)
),
plot.tag = element_text(
face = "bold",
hjust = 0, vjust = 0.7
),
plot.tag.position = c(0, 1),
plot.margin = margin(half_line, half_line, half_line, half_line),
complete = TRUE
)
}
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