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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,125 +1,158 @@ | ||
| # figure specs | ||
| fig_spec <- list() | ||
|
|
||
| # ggplot theme ---------------------------------------------------- | ||
|
|
||
| # ggplot theme by Jonas Schöley | ||
| fig_spec$MyGGplotTheme <- | ||
| function ( | ||
| size = 8, | ||
| family = 'sans', | ||
| scaler = 1, | ||
| no_axes = FALSE, | ||
| panel_border = FALSE, | ||
| hgrid = FALSE, | ||
| vgrid = FALSE, | ||
| show_legend = TRUE, | ||
| ar = NA | ||
| ) { | ||
|
|
||
| size_med = size*scaler | ||
| size_sml = round(size*0.7)*scaler | ||
| base_linesize = 0.3*scaler | ||
|
|
||
| list( | ||
| theme_classic(base_size = size_med, base_family = family), | ||
| theme( | ||
| # basic | ||
| text = element_text(color = 'black'), | ||
| line = element_line(size = base_linesize, lineend = 'square'), | ||
| # axis | ||
| #axis.line.y = element_blank(), | ||
| axis.title = element_text(size = size_med, face = 'bold'), | ||
| axis.ticks = element_line(size = rel(0.5), color = 'black'), | ||
| axis.text = element_text(size = size_med, color = 'black'), | ||
| # strips | ||
| strip.text = element_text(color = 'black', size = size_med), | ||
| strip.background = element_blank(), | ||
| # plot | ||
| title = element_text(face = 'bold'), | ||
| plot.subtitle = element_text(color = 'black', size = size_med, face = 'bold'), | ||
| plot.caption = element_text(color = 'black', size = size_sml, face = 'plain'), | ||
| plot.background = element_blank(), | ||
| panel.background = element_blank(), | ||
| plot.margin = unit(c(1, 0.1, 0.5, 0.5), units = 'mm'), | ||
| ), | ||
| if (isTRUE(hgrid)) { | ||
| theme(panel.grid.major.y = | ||
| element_line(linetype = 3, color = 'grey80')) | ||
| }, | ||
| if (isTRUE(vgrid)) { | ||
| theme(panel.grid.major.x = | ||
| element_line(linetype = 3, color = 'grey80')) | ||
| }, | ||
| if (isTRUE(panel_border)) { | ||
| theme( | ||
| panel.border = | ||
| element_rect(fill = NA) | ||
| ) | ||
| }, | ||
| if (!isTRUE(show_legend)) { | ||
| theme(legend.position = 'none') | ||
| }, | ||
| if (isTRUE(no_axes)) { | ||
| theme( | ||
| axis.line = element_blank() | ||
| ) | ||
| }, | ||
| if (!is.na(ar)) { | ||
| theme( | ||
| aspect.ratio = ar | ||
| ) | ||
| } | ||
| ) | ||
| } | ||
|
|
||
| # Dimensions ------------------------------------------------------ | ||
|
|
||
| # figure width (mm) | ||
| fig_spec$width = 170 | ||
|
|
||
| # Colors ---------------------------------------------------------- | ||
|
|
||
| # color palette | ||
| fig_spec$discrete_colors <- | ||
| c('#D23737', # red | ||
| '#3191C9', # blue | ||
| '#D2BC2D', # yellow | ||
| '#4EC93B', # green | ||
| '#881F93', # purple | ||
| '#C5752B') # orange | ||
| fig_spec$discrete_colors_light <- | ||
| c('#FCB3B3', # red | ||
| '#A7DDFC', # blue | ||
| '#FAEC8E' # yellow | ||
| ) | ||
|
|
||
| fig_spec$sex_colors <- | ||
| c(`m` = '#806152', `f` = '#1E8B8F') | ||
|
|
||
| # Export function ------------------------------------------------- | ||
|
|
||
| fig_spec$ExportPDF <- | ||
| function (figure, filename, path, ...) { | ||
| ggsave( | ||
| filename = paste0(filename, '.pdf'), | ||
| plot = figure, | ||
| path = path, | ||
| units = 'mm', | ||
| dpi = 300, | ||
| useDingbats = FALSE, | ||
| ... | ||
| ) | ||
| } | ||
|
|
||
| fig_spec$ExportPNG <- | ||
| function (figure, filename, path, ...) { | ||
| ggsave( | ||
| filename = paste0(filename, '.png'), | ||
| plot = figure, | ||
| path = path, | ||
| units = 'mm', | ||
| dpi = 300, | ||
| ... | ||
| ) | ||
| } | ||
| # figure specs | ||
| fig_spec <- list() | ||
|
|
||
| # ggplot theme ---------------------------------------------------- | ||
|
|
||
| # ggplot theme by Jonas Schöley | ||
| fig_spec$MyGGplotTheme <- | ||
| function ( | ||
| size = 8, | ||
| family = 'sans', | ||
| scaler = 1, | ||
| axis = 'x', | ||
| panel_border = FALSE, | ||
| grid = 'y', | ||
| minor_grid = '', | ||
| show_legend = TRUE, | ||
| ar = NA | ||
| ) { | ||
|
|
||
| size_med = size*scaler | ||
| size_sml = round(size*0.7)*scaler | ||
| base_linesize = 0.3*scaler | ||
|
|
||
| list( | ||
| theme_minimal(base_size = size_med, base_family = family), | ||
| theme( | ||
| # basic | ||
| text = element_text(color = 'black'), | ||
| line = element_line(size = base_linesize, lineend = 'square'), | ||
| # axis | ||
| #axis.line.y = element_blank(), | ||
| axis.title = element_text(size = size_med, face = 'bold'), | ||
| #axis.ticks = element_line(size = rel(0.5), color = 'black'), | ||
| axis.text = element_text(size = size_med, color = 'black'), | ||
| # strips | ||
| strip.text = element_text(color = 'black', size = size_med), | ||
| strip.background = element_blank(), | ||
| # plot | ||
| title = element_text(face = 'bold'), | ||
| plot.subtitle = element_text(color = 'black', size = size_med, face = 'bold'), | ||
| plot.caption = element_text(color = 'black', size = size_sml, face = 'plain'), | ||
| plot.background = element_blank(), | ||
| panel.background = element_blank(), | ||
| #plot.margin = unit(c(1, 0.1, 0.5, 0.5), units = 'mm'), | ||
| # grid | ||
| panel.grid = element_blank() | ||
| ), | ||
| if (identical(grid, 'y')) { | ||
| theme(panel.grid.major.y = | ||
| element_line(size = base_linesize, linetype = 3, color = 'grey80')) | ||
| }, | ||
| if (identical(grid, 'x')) { | ||
| theme(panel.grid.major.x = | ||
| element_line(size = base_linesize, linetype = 3, color = 'grey80')) | ||
| }, | ||
| if (identical(grid, 'xy') | identical(grid, 'yx')) { | ||
| theme(panel.grid.major.y = | ||
| element_line(size = base_linesize, linetype = 3, color = 'grey80'), | ||
| panel.grid.major.x = | ||
| element_line(size = base_linesize, linetype = 3, color = 'grey80')) | ||
| }, | ||
| if (identical(minor_grid, 'y')) { | ||
| theme(panel.grid.minor.y = | ||
| element_line(size = base_linesize, linetype = 3, color = 'grey80')) | ||
| }, | ||
| if (identical(minor_grid, 'x')) { | ||
| theme(panel.grid.minor.x = | ||
| element_line(size = base_linesize, linetype = 3, color = 'grey80')) | ||
| }, | ||
| if (identical(minor_grid, 'xy') | identical(grid, 'yx')) { | ||
| theme(panel.grid.minor.y = | ||
| element_line(size = base_linesize, linetype = 3, color = 'grey80'), | ||
| panel.grid.minor.x = | ||
| element_line(size = base_linesize, linetype = 3, color = 'grey80')) | ||
| }, | ||
| if (isTRUE(panel_border)) { | ||
| theme( | ||
| panel.border = | ||
| element_rect(fill = NA) | ||
| ) | ||
| }, | ||
| if (!isTRUE(show_legend)) { | ||
| theme(legend.position = 'none') | ||
| }, | ||
| if (axis == 'x') { | ||
| theme( | ||
| axis.line.x = element_line(linetype = 1, color = 'black') | ||
| ) | ||
| }, | ||
| if (axis == 'y') { | ||
| theme( | ||
| axis.line.y = element_line(linetype = 1, color = 'black') | ||
| ) | ||
| }, | ||
| if (axis == 'xy') { | ||
| theme( | ||
| axis.line = element_line(linetype = 1, color = 'black') | ||
| ) | ||
| }, | ||
| if (!is.na(ar)) { | ||
| theme( | ||
| aspect.ratio = ar | ||
| ) | ||
| } | ||
| ) | ||
| } | ||
|
|
||
|
|
||
| # Dimensions ------------------------------------------------------ | ||
|
|
||
| # figure width (mm) | ||
| fig_spec$width = 170 | ||
|
|
||
| # Colors ---------------------------------------------------------- | ||
|
|
||
| # color palette | ||
| fig_spec$discrete_colors <- | ||
| c('#D23737', # red | ||
| '#3191C9', # blue | ||
| '#D2BC2D', # yellow | ||
| '#4EC93B', # green | ||
| '#881F93', # purple | ||
| '#C5752B') # orange | ||
| fig_spec$discrete_colors_light <- | ||
| c('#FCB3B3', # red | ||
| '#A7DDFC', # blue | ||
| '#FAEC8E' # yellow | ||
| ) | ||
|
|
||
| fig_spec$sex_colors <- | ||
| c(`m` = '#806152', `f` = '#1E8B8F') | ||
|
|
||
| # Export function ------------------------------------------------- | ||
|
|
||
| fig_spec$ExportPDF <- | ||
| function (figure, filename, path, ...) { | ||
| ggsave( | ||
| filename = paste0(filename, '.pdf'), | ||
| plot = figure, | ||
| path = path, | ||
| units = 'mm', | ||
| dpi = 300, | ||
| useDingbats = FALSE, | ||
| ... | ||
| ) | ||
| } | ||
|
|
||
| fig_spec$ExportPNG <- | ||
| function (figure, filename, path, ...) { | ||
| ggsave( | ||
| filename = paste0(filename, '.png'), | ||
| plot = figure, | ||
| path = path, | ||
| units = 'mm', | ||
| dpi = 300, | ||
| ... | ||
| ) | ||
| } |