| forest_plot {coveffectsplot} | R Documentation |
Forest plot
Description
Produce forest plots to visualize covariate effects
Usage
forest_plot(
data,
facet_formula = "covname~paramname",
xlabel = "",
ylabel = "",
x_facet_text_size = 13,
y_facet_text_size = 13,
x_facet_text_angle = 0,
y_facet_text_angle = 0,
x_facet_text_vjust = 0.5,
y_facet_text_vjust = 0.5,
x_facet_text_hjust = 0.5,
y_facet_text_hjust = 0.5,
x_facet_text_col = "black",
y_facet_text_col = "black",
xy_facet_text_bold = TRUE,
x_label_text_size = 16,
y_label_text_size = 16,
legend_title_size = 12,
break_ylabel = FALSE,
y_label_text_width = 25,
table_text_size = 7,
table_text_colour_overwrite = FALSE,
table_text_colour = "none",
base_size = 22,
theme_benrich = FALSE,
table_title = "",
table_title_size = 15,
ref_legend_text = "",
area_legend_text = "",
interval_legend_text = "",
interval_legend_title = "",
shape_legend_title = "",
legend_order = c("pointinterval", "ref", "area", "shape"),
combine_area_ref_legend = TRUE,
combine_interval_shape_legend = FALSE,
legend_position = "top",
show_ref_area = TRUE,
ref_area = c(0.8, 1.25),
ref_area_col = "#BEBEBE50",
show_ref_value = TRUE,
ref_value = 1,
ref_value_col = "black",
ref_value_size = 1,
ref_value_linetype = "dashed",
ref_value_by_panel = FALSE,
ref_value_by_panel_data = NULL,
interval_col = "blue",
interval_size = 1,
interval_fatten = 4,
interval_linewidth = 1,
interval_shape = "circle small",
bsv_col = "red",
bsv_shape = "circle small",
bsv_text_id = c("BSV", "bsv", "IIV", "Bsv"),
interval_bsv_text = "",
strip_col = "#E5E5E5",
paramname_shape = FALSE,
paramname_color = FALSE,
legend_shape_reverse = FALSE,
legend_color_reverse = FALSE,
facet_switch = c("both", "y", "x", "none"),
facet_scales = c("fixed", "free_y", "free_x", "free"),
facet_space = c("fixed", "free_x", "free_y", "free"),
facet_labeller = "label_value",
label_wrap_width = 55,
facet_labeller_multiline = FALSE,
strip_placement = c("inside", "outside"),
strip_outline = TRUE,
facet_spacing = 5.5,
major_x_ticks = NULL,
major_x_labels = NULL,
minor_x_ticks = NULL,
x_range = NULL,
logxscale = FALSE,
show_yaxis_gridlines = TRUE,
show_xaxis_gridlines = TRUE,
show_table_facet_strip = "none",
table_facet_switch = c("both", "y", "x", "none"),
show_table_yaxis_tick_label = FALSE,
reserve_table_xaxis_label_space = TRUE,
table_panel_border = TRUE,
table_position = c("right", "below", "none"),
plot_table_ratio = 4,
vertical_dodge_height = 0.8,
legend_space_x_mult = 1,
legend_ncol_interval = 1,
legend_ncol_shape = 1,
plot_margin = c(5.5, 5.5, 5.5, 5.5),
table_margin = c(5.5, 5.5, 5.5, 5.5),
legend_margin = c(0, 0.1, -0.1, 0),
parse_xlabel = FALSE,
parse_ylabel = FALSE,
plot_title = "\n",
return_list = FALSE
)
Arguments
data |
Data to use. |
facet_formula |
Facet formula. |
xlabel |
X axis title. |
ylabel |
Y axis title. |
x_facet_text_size |
Facet text size X. |
y_facet_text_size |
Facet text size Y. |
x_facet_text_angle |
Facet text angle X. |
y_facet_text_angle |
Facet text angle Y. |
x_facet_text_vjust |
Facet text vertical justification. |
y_facet_text_vjust |
Facet text vertical justification. |
x_facet_text_hjust |
Facet text horizontal justification. |
y_facet_text_hjust |
Facet text horizontal justification. |
x_facet_text_col |
Facet text color default to black. |
y_facet_text_col |
Facet text color default to black. |
xy_facet_text_bold |
Bold Facet text. Logical TRUE FALSE. |
x_label_text_size |
X axis labels size. |
y_label_text_size |
Y axis labels size. |
legend_title_size |
Legend title size if present. |
break_ylabel |
Split Y axis labels into multiple lines. Logical FALSE TRUE. |
y_label_text_width |
Number of characters to break Y axis labels. |
table_text_size |
Table text size. |
table_text_colour_overwrite |
Logical TRUE FALSE. |
table_text_colour |
Table text color to be used and overwrites mapped color |
base_size |
theme_bw base_size for the plot and table. |
theme_benrich |
apply Benjamin Rich's theming. |
table_title |
What text to use for table title (theme_benrich has a default). |
table_title_size |
table title size. |
ref_legend_text |
Reference legend text. |
area_legend_text |
Area legend text. |
interval_legend_text |
Pointinterval legend text. |
interval_legend_title |
Pointinterval legend title defaults to empty. |
shape_legend_title |
Shape legend title defaults to empty. |
legend_order |
Legend order. A four-element vector with the following items ordered in your desired order: "pointinterval", "ref", "area", "shape". if an item is absent the legend will be omitted. |
combine_area_ref_legend |
Combine reference and area legends if they share the same text? |
combine_interval_shape_legend |
Combine interval and shape legends? |
legend_position |
where to put the legend: "top", "bottom","right","none" |
show_ref_area |
Show reference window? |
ref_area |
Reference area. Two-element numeric vector multiplying the ref_value. |
ref_area_col |
Reference area background color. |
show_ref_value |
Show reference line? |
ref_value |
X intercept of reference line. |
ref_value_col |
Reference line color. |
ref_value_size |
Reference line size. |
ref_value_linetype |
Reference line linetype. |
ref_value_by_panel |
The ref_value vary by panel TRUE or FALSE. |
ref_value_by_panel_data |
if ref_value_by_panel is TRUE, data.frame to use for Reference (lines). |
interval_col |
Point range color. One or Multiple values. |
interval_size |
Point range size. Default to 1 |
interval_fatten |
Point range fatten. Default to 4 |
interval_linewidth |
Point range line width. Default to 1 |
interval_shape |
Shape used for the Point Range. Default to "circle small". |
bsv_col |
BSV pointinterval color. One value. |
bsv_shape |
Shape used for the BSV Point Range. Default to "circle small". |
bsv_text_id |
Text string(s) to identify BSV. Default to c("BSV","bsv","IIV","Bsv") |
interval_bsv_text |
BSV legend text. |
strip_col |
Strip background color. |
paramname_shape |
Map symbol to parameter(s) name? TRUE or FALSE. |
paramname_color |
Map color to parameter(s) name? TRUE or FALSE. |
legend_shape_reverse |
TRUE or FALSE. |
legend_color_reverse |
TRUE or FALSE. |
facet_switch |
Facet switch to near axis. Possible values: "both", "y", "x", "none". |
facet_scales |
Facet scales. Possible values: "free_y", "fixed", "free_x", "free". |
facet_space |
Facet spaces. Possible values: "fixed", "free_x", "free_y", "free". |
facet_labeller |
Facet Labeller. Default "label_value" any other valid 'facet_grid' labeller can be specified. |
label_wrap_width |
How many characters before breaking the line. Numeric value. any other valid 'facet_grid' labeller can be specified. |
facet_labeller_multiline |
break facet strips into multiple lines. Logical TRUE FALSE. |
strip_placement |
Strip placement. Possible values: "inside", "outside". |
strip_outline |
Draw rectangle around the Strip. Logical TRUE FALSE. |
facet_spacing |
Control the space between facets in points. |
major_x_ticks |
X axis major ticks. Numeric vector. |
major_x_labels |
X axis labels. Character vector should be same length as major_x_ticks. |
minor_x_ticks |
X axis minor ticks. Numeric vector. |
x_range |
Range of X values. Two-element numeric vector. |
logxscale |
X axis log scale. Logical TRUE FALSE. |
show_yaxis_gridlines |
Draw the y axis gridlines. Logical TRUE FALSE. |
show_xaxis_gridlines |
Draw the x axis gridlines. Logical TRUE FALSE. |
show_table_facet_strip |
Possible values: "none", "both", "y", "x". |
table_facet_switch |
Table facet switch to near axis. Possible values: "both", "y", "x", "none". |
show_table_yaxis_tick_label |
Show table y axis ticks and labels? |
reserve_table_xaxis_label_space |
keep space for the x axis label to keep alignment. |
table_panel_border |
Draw the panel border for the table. Logical TRUE FALSE. |
table_position |
Table position. Possible values: "right", "below", "none". |
plot_table_ratio |
Plot-to-table ratio. Suggested value between 1-5. |
vertical_dodge_height |
Amount of vertical dodging to apply on segments and table text. |
legend_space_x_mult |
Multiplier to adjust the spacing between legend items. |
legend_ncol_interval |
Control the number of columns for the pointinterval legend. |
legend_ncol_shape |
Control the number of columns for the shape legend. |
plot_margin |
Control the white space around the main plot. Vector of four numeric values for the top, right, bottom and left sides. |
table_margin |
Control the white space around the table. Vector of four numeric values for the top, right, bottom and left sides. |
legend_margin |
Control the white space around the plot legend. Vector of four numeric values for the top, right, bottom and left sides. |
parse_xlabel |
treat xlabel as an expression. Logical FALSE TRUE. |
parse_ylabel |
treat ylabel as an expression. Logical FALSE TRUE. |
plot_title |
main plot title default to a line break. |
return_list |
What to return if True a list of the main and table plots is returned instead of the gtable/plot. |
Examples
library(dplyr)
library(ggplot2)
# Example 1
plotdata <- get_sample_data("forest-plot-table.csv")
plotdata <- plotdata %>%
mutate(midlabel = format(round(mid,2), nsmall = 2),
lowerlabel = format(round(lower,2), nsmall = 2),
upperlabel = format(round(upper,2), nsmall = 2),
LABEL = paste0(midlabel, " [", lowerlabel, "-", upperlabel, "]"))
param <- "BZD AUC"
plotdata <- filter(plotdata,paramname==param)
plotdata$covname <- reorder(plotdata$covname,plotdata$upper,FUN =max)
plotdata$label <- reorder(plotdata$label,plotdata$scen)
covs <- c("WEIGHT","AGE")
plotdata <- filter(plotdata,covname%in%covs)
forest_plot(plotdata,
ref_legend_text = "Reference (vertical line)",
area_legend_text = "Reference (vertical line)",
xlabel = paste("Fold Change in", param, "Relative to Reference"),
logxscale = TRUE, major_x_ticks =c(0.1,1,1.5),
show_ref_area = FALSE,
paramname_color =TRUE,
interval_col =c("steelblue","red","steelblue","red"),
facet_formula = "covname~.",
facet_scales = "free_y",
facet_space = "free_y",
show_table_facet_strip = "none",
table_position = "right",
plot_title = "",
plot_table_ratio = 4)
# Example 2
plotdata <- get_sample_data("forest-plot-table.csv")
plotdata <- plotdata %>%
mutate(midlabel = format(round(mid,2), nsmall = 2),
lowerlabel = format(round(lower,2), nsmall = 2),
upperlabel = format(round(upper,2), nsmall = 2),
LABEL = paste0(midlabel, " [", lowerlabel, "-", upperlabel, "]"))
param <- c("BZD AUC","BZD Cmax")
plotdata <- filter(plotdata,paramname%in%param)
plotdata <- filter(plotdata,covname%in%"WEIGHT")
plotdata$covname <- reorder(plotdata$covname,plotdata$upper,FUN =max)
plotdata$label <- reorder(plotdata$label,plotdata$scen)
forest_plot(plotdata,
ref_legend_text = "Reference (vertical line)",
area_legend_text = "Reference (vertical line)",
xlabel = paste("Fold Change of Parameter", "Relative to Reference"),
show_ref_area = FALSE,
facet_formula = "covname~paramname",
facet_scales = "free_y",
facet_space = "free_y",
x_facet_text_size = 10,
y_facet_text_size = 10,
y_label_text_size = 10,
y_label_text_width = 15,
x_label_text_size = 10,
facet_switch = "both",
show_table_facet_strip = "both",
show_table_yaxis_tick_label = TRUE,
table_position = "below",
plot_title = "",
plot_table_ratio = 1)
## Not run:
# Example 3a
plotdata <- get_sample_data("forest-plot-table.csv")
plotdata <- plotdata %>%
mutate(midlabel = format(round(mid,2), nsmall = 2),
lowerlabel = format(round(lower,2), nsmall = 2),
upperlabel = format(round(upper,2), nsmall = 2),
LABEL = paste0(midlabel, " [", lowerlabel, "-", upperlabel, "]"))
plotdata$covname <- reorder(plotdata$covname,plotdata$upper,FUN =max)
plotdata$label <- reorder(plotdata$label,plotdata$scen)
plotdata$compound <- c(rep("1-OH",30),rep("BZD",30))
plotdata$paramname <- c(rep("AUC",15),rep("CMAX",15),rep("AUC",15),rep("CMAX",15))
forest_plot(plotdata,
ref_area = c(0.8, 1.2),
x_facet_text_size = 13,
y_facet_text_size = 13,
ref_legend_text = "Reference (vertical line)\n+/- 20% limits (colored area)",
area_legend_text = "Reference (vertical line)\n+/- 20% limits (colored area)",
xlabel = "Fold Change Relative to Parameter",
facet_formula = covname~compound,
facet_switch = "both",
facet_scales = "free",
facet_space = "fixed",
paramname_shape = TRUE,
legend_shape_reverse = TRUE,
interval_shape = c("square","triangle"),
paramname_color = FALSE,
combine_interval_shape_legend = FALSE,
table_position = "right", plot_title = "",
ref_area_col = rgb( col2rgb("gray50")[1], col2rgb("gray50")[2],col2rgb("gray50")[3],
max = 255, alpha = 0.1*255 ) ,
interval_col = c("steelblue"),
strip_col = "lightblue",
plot_table_ratio = 1.5)
# Example 3b
plotdata$paramname <- c(rep("1-OH",30),rep("BZD",30))
plotdata$paramname2 <- c(rep("AUC",15),rep("CMAX",15),rep("AUC",15),rep("CMAX",15))
forest_plot(plotdata,
show_ref_area = TRUE,
x_facet_text_size = 13,
y_facet_text_size = 13,
ref_legend_text = "Reference (vertical line)",
area_legend_text = "Reference (vertical line)",
xlabel = "Fold Change Relative to Parameter",
facet_formula = covname~paramname2,
facet_switch = "both",
facet_scales = "free",
facet_space = "free",
legend_order = c("shape","pointinterval","ref"),
paramname_shape = TRUE,
interval_shape = c("diamond","diamond filled",
"diamond","diamond filled"),
paramname_color = TRUE,
combine_interval_shape_legend = TRUE,
legend_shape_reverse = TRUE,
legend_color_reverse = TRUE,
interval_legend_title="Median (points)\n95% CI (horizontal lines)",
table_position = "right", plot_title = "",
ref_area_col = "gray85" ,
interval_col = c("#ee3124", "#fdbb2f"),
strip_col = "#475c6b",
y_facet_text_col = "white",x_facet_text_col = "white",
major_x_labels = c("1/2", "0.8","1", "1.25", "2"),
logxscale = TRUE, major_x_ticks =c(0.5,0.8,1,1.25,2),
table_text_size = 5,
plot_table_ratio = 1.5,
ref_value_by_panel = TRUE,
ref_value_by_panel_data = as.data.frame(
plotdata %>%
distinct(paramname2,covname) %>%
dplyr::mutate(xintercept=ifelse(paramname2=="CMAX",1,1.2))))
# Example 3
plotdata <- get_sample_data("forestplotdatacpidata.csv")
forest_plot(plotdata,
ref_area = c(0.8, 1.2),
x_facet_text_size = 12,
y_facet_text_size = 12,
y_label_text_size = 10,
x_label_text_size = 10,
table_text_size = 6,
plot_table_ratio = 1.5,
ref_legend_text = "Reference (vertical line)\n+/- 20% limits (colored area)",
area_legend_text = "Reference (vertical line)\n+/- 20% limits (colored area)",
xlabel = "Fold Change Relative to RHZE",
facet_formula = "covname~paramname",
table_position = "below",
show_table_facet_strip = "both",
show_table_yaxis_tick_label = TRUE)
# Example 4
plotdata <- get_sample_data("dataforest.csv")
plotdata <- plotdata %>%
dplyr::mutate(midlabel = format(round(mid,2), nsmall = 2),
lowerlabel = format(round(lower,2), nsmall = 2),
upperlabel = format(round(upper,2), nsmall = 2),
LABEL = paste0(midlabel, " [", lowerlabel, "-", upperlabel, "]"))
plotdata <- plotdata %>%
filter(covname%in%c("Weight"))
plotdata$label <- as.factor(as.character(plotdata$label))
plotdata$label <- factor(plotdata$label, c("36.2 kg","66 kg","110 kg"))
forest_plot(plotdata,
ref_area = c(0.8, 1.2),
x_facet_text_size = 13,
y_facet_text_size = 13,
ref_legend_text = "Reference (vertical line)\n+/- 20% limits (colored area)",
area_legend_text = "Reference (vertical line)\n+/- 20% limits (colored area)",
xlabel = "Fold Change Relative to Parameter",
facet_formula = "covname~paramname",
facet_switch = "both",
facet_scales = "free",
facet_space = "fixed",
table_position = "below",
plot_table_ratio = 1,
show_table_facet_strip = "both",
show_table_yaxis_tick_label = TRUE)
# Example 5
forest_plot(plotdata,
ref_area = c(0.8, 1.2),
x_facet_text_size = 13,
y_facet_text_size = 13,
ref_legend_text = "Reference (vertical line)\n+/- 20% limits (colored area)",
area_legend_text = "Reference (vertical line)\n+/- 20% limits (colored area)",
xlabel = "Fold Change Relative to Parameter",
facet_formula = "covname~.",
facet_switch = "both",
facet_scales = "free",
facet_space = "fixed",
paramname_shape = TRUE,
table_position = "none",
ref_area_col = rgb( col2rgb("gray50")[1], col2rgb("gray50")[2],col2rgb("gray50")[3],
max = 255, alpha = 0.1*255 ) ,
interval_col = "steelblue",
strip_col = "lightblue",
plot_table_ratio = 1)
## End(Not run)