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Spider Plot

Source: R/g_spiderplot.R
g_spiderplot.Rd

Spider plot is often used in Early Development (ED) and displays individual patient plot of an endpoint over time by group.

Usage

g_spiderplot(
  marker_x,
  marker_id,
  marker_y,
  line_colby = NULL,
  line_color_opt = NULL,
  marker_shape = NULL,
  marker_shape_opt = NULL,
  marker_size = 3,
  datalabel_txt = NULL,
  facet_rows = NULL,
  facet_columns = NULL,
  vref_line = NULL,
  href_line = NULL,
  x_label = "Time (Days)",
  y_label = "Change (%) from Baseline",
  show_legend = FALSE
)

Arguments

marker_x

vector of x values (must be in sorted order)

marker_id

vector to group the points together (default should be USUBJID)

marker_y

vector of y values

line_colby

vector defines by what variable plot is color coded, default here is NULL

line_color_opt

vector defines line color, default here is NULL

marker_shape

vector defines by what variable points are shape coded, , default here is NULL

marker_shape_opt

vector defines marker shape code, default here is NULL

marker_size

size of markers in plot, default here is NULL

datalabel_txt

list defines text (at last time point) and flag for an arrow annotation:

  • (per defined variable) elements must be labeled txt_ann/mrkr_all/mrkr_ann.

  • txt_ann text annotation next to final data point (for text annotation)

  • mrkr_all vector of ID's (for annotation marker)

  • mrkr_ann vector of ID's (subset of mrkr_all) where arrow is desired to indicate any study interim points. Default here is NULL.

facet_rows

dataframe defines what variable is used to split the plot into rows, default here is NULL.

facet_columns

dataframe defines what variable is used to split the plot into columns, default here is NULL.

vref_line

value defines vertical line overlay (can be a vector), default here is NULL.

href_line

value defines horizontal line overlay (can be a vector), default here is NULL.

x_label

string of text for x axis label, default is time.

y_label

string of text for y axis label, default is % change.

show_legend

boolean of whether marker legend is included, default here is FALSE.

Value

ggplot object

Details

there is no equivalent STREAM output

Author

Carolyn Zhang (zhanc107) carolyn.zhang@duke.edu

Examples

# simple example
library(dplyr)
library(nestcolor)

ADTR <- osprey::rADTR %>% select(STUDYID, USUBJID, ADY, AVISIT, CHG, PCHG, PARAMCD)
ADSL <- osprey::rADSL %>% select(STUDYID, USUBJID, RACE, SEX, ARM)
ANL <- left_join(ADTR, ADSL, by = c("STUDYID", "USUBJID"))
ANL <- ANL %>%
  dplyr::filter(PARAMCD == "SLDINV" & AVISIT != "POST-BASELINE MINIMUM") %>%
  dplyr::filter(RACE %in% c("WHITE", "ASIAN")) %>%
  group_by(USUBJID) %>%
  dplyr::arrange(ADY) %>%
  dplyr::mutate(
    CHG = ifelse(AVISIT == "Screening", 0, CHG),
    PCHG = ifelse(AVISIT == "Screening", 0, PCHG)
  )
ANL$USUBJID <- substr(ANL$USUBJID, 14, 18)

# Plot 1 - default color and shape mapping
g_spiderplot(
  marker_x = ANL$ADY,
  marker_id = ANL$USUBJID,
  marker_y = ANL$PCHG,
  line_colby = ANL$USUBJID,
  marker_shape = ANL$USUBJID,
  # marker_size = 5,
  datalabel_txt = list(txt_ann = ANL$USUBJID),
  # facet_rows = data.frame(sex = ANL$SEX),
  # facet_columns = data.frame(arm = ANL$ARM),
  vref_line = c(42, 86),
  href_line = c(-20, 20),
  x_label = "Time (Days)",
  y_label = "Change (%) from Baseline",
  show_legend = TRUE
)
#> Warning: Removed 554 rows containing missing values (`geom_line()`).
#> Warning: Removed 568 rows containing missing values (`geom_point()`).
#> Warning: Removed 564 rows containing missing values (`geom_text()`).


# Plot 2 - with line color mapping
g_spiderplot(
  marker_x = ANL$AVISIT,
  marker_id = ANL$USUBJID,
  marker_y = ANL$CHG,
  line_colby = ANL$RACE,
  line_color_opt = c("WHITE" = "red", "ASIAN" = "blue"),
  marker_shape = ANL$USUBJID,
  x_label = "Visit",
  y_label = "Change from Baseline",
  show_legend = TRUE
)
#> Warning: Removed 564 rows containing missing values (`geom_line()`).
#> Warning: Removed 568 rows containing missing values (`geom_point()`).