Mapping error connectGrob when spreadHorizontal is used #68
Description
Hi Gmisc,
Thanks for coming up with this fantastic package. I had a great time with it.
I noticed that when connecting boxGrobs that have been spreadHorizontal, the package maps the initial position of the boxGrob instead of the new position after being evenly spread. I've attached the initial flow analysis diagram with the error I've noted above and a second script where I had to create transparent dummy boxGrox with alpha = 0.01. This helped with mapping the new/correct positions of the boxGrobs after spreadHorizontal function.
Also to mention that we used this package for this analysis: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0306131
I couldn't attached the R script, the code is below:
# 1. Clear console and environment -------------------------------------------
rm(list=ls(all=T)) #clear environment
cat("\f") #clear console
# 2. Install and load packages -----------------------------------------------
pacman::p_load(survey, # Contains survey analysis specific functions
dplyr, # Package for data manipulation
rio, # Allows user to import files from Stata and SPSS, optional
haven, # Allows import of stata dta
gmodels, # Unweighted tables of proportions and frequencies
expss, # Apply labels
tidyverse,
janitor,
haven,
visdat,
readr,
gtsummary)
# 3. Create a flowchart --------------------------------------------------
pacman::p_load(Gmisc,
glue,
htmlTable,
grid,
magrittr)
# browseURL("https://cran.r-project.org/web/packages/Gmisc/vignettes/Grid-based_flowcharts.html")
# 4. Original flow diagram with the noted error ---------------------------
grid.newpage()
txt1 <- "1,359 patients who attended PAC-19\n clinics from Aug-2020 to Jan-2023\n had their data entered in REDCap\n electronic database "
org_cohort <- boxGrob(txt1,
x = 0.5, y = .91,
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white", col = "black"))
org_cohort
txt2 <- "\n 1,359 (100%) PAC-19 clinic patients \n in REDCap electronic database"
xsec_study1 <- boxGrob(txt2,
x = 0.5,
y = coords(org_cohort)$bottom - distance(org_cohort,
org_cohort,
type = "h",
half = T) +
unit(5, "mm"),
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white", col = "black"))
xsec_study1
# Connect the boxes and print/plot them
connectGrob(org_cohort, xsec_study1, "vertical")
xsec_study2 <- boxGrob(expression(paste(bold("Cross-sectional analysis:"))),
x = 0.5,
y = coords(xsec_study1)$top - unit(5, "mm"),
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(col = "white", fill = "white", alpha = 0.1))
xsec_study2
txt3 <- "811 (59.7%) had only one \nPAC-19 clinic visit"
exclude_cohort <- boxGrob(txt3,
x = 0.8,
y = coords(xsec_study1)$top - distance(xsec_study1,
xsec_study1,
type = "h",
half = T) +
unit(5, "mm"),
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
exclude_cohort
# Connect the boxes and print/plot them
connectGrob(xsec_study1, exclude_cohort, "L")
long_study <- boxGrob(expression(paste(bold("Longitudinal analysis"))),
x = 0.5,
y = coords(exclude_cohort)$top - distance(exclude_cohort,
exclude_cohort,
type = "h",
half = T) -
unit(5, "mm"),
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(col = "white", fill = "white", alpha = 0.1))
long_study
# Connect the boxes and print/plot them
connectGrob(xsec_study1, long_study, "vertical")
txt4 <- "Visit 1:"
txt5 <- "548 (100%)"
visit1_a <- boxGrob(paste(c(txt4, txt5), collapse = "\n"),
x = 0.05,
y = coords(long_study)$bottom - 0.6*coords(long_study)$height,
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
txt6 <- "Visit 5:"
txt7 <- "50 (43.5%)"
visit5 <- boxGrob(paste(c(txt6, txt7), collapse = "\n"),
x = 0.95,
y = coords(long_study)$bottom - 0.6*coords(long_study)$height,
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
txt8 <- "Visit 2:"
txt9 <- "548 (100%)"
visit2_a <- boxGrob(paste(c(txt8, txt9), collapse = "\n"),
x = coords(visit1_a)$right + 7.4*distance(visit1_a,
visit1_a,
type = "v",
half = T),
y = coords(long_study)$bottom - 0.6*coords(long_study)$height,
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
txt10 <- "Visit 3:"
txt11 <- "234 (42.7%)"
visit3_a <- boxGrob(paste(c(txt10, txt11), collapse = "\n"),
x = 0.5,
y = coords(long_study)$bottom - 0.6*coords(long_study)$height,
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
txt12 <- "Visit 4:"
txt13 <- "115 (49.1%)"
visit4_a <- boxGrob(paste(c(txt12, txt13), collapse = "\n"),
x = 0.7,
y = coords(long_study)$bottom - 0.6*coords(long_study)$height,
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
visit1_a
visit5
alignVertical(reference = visit1_a,
visit2_a, visit3_a, visit4_a,
.position = "top") %>%
spreadHorizontal(.from = visit1_a,
.to = visit5)
# Connect the boxes and print/plot them
connectGrob(visit1_a, visit2_a, "horizontal") #visit2_a is mapped to the original position
connectGrob(visit2_a, visit3_a, "horizontal") #visit3_a is mapped to the original position
connectGrob(visit3_a, visit4_a, "horizontal") #visit4_a is mapped to the original position
connectGrob(visit4_a, visit5, "horizontal")
txt14 <- "Discharged"
txt15 <- "216 (39.4%)"
txt16 <- "Lost to follow up"
txt17 <- "98 (17.9%)"
dchrg1 <- boxGrob(paste(c(txt14, txt15, txt16, txt17), collapse = "\n"),
x = coords(visit2_a)$right + unit(20, "mm"),
y = coords(visit2_a)$bottom - 1.7*distance(visit2_a,
visit2_a,
type = "h",
half = T),
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
dchrg1
# Connect the boxes and print/plot them
connectGrob(visit2_a, dchrg1, "L")
txt18 <- "78 (33.3%)"
txt19 <- "41 (17.6%)"
dchrg3 <- boxGrob(paste(c(txt14, txt18, txt16, txt19), collapse = "\n"),
x = coords(visit3_a)$right + unit(20, "mm"),
y = coords(visit2_a)$bottom - 1.7*distance(visit2_a,
visit2_a,
type = "h",
half = T),
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
dchrg3
# Connect the boxes and print/plot them
connectGrob(visit3_a, dchrg3, "L")
dchrg4 <- boxGrob(paste(c(txt14)),
x = coords(visit3_a)$right + unit(20, "mm"),
y = coords(visit3_a)$top - unit(3.1, "mm"),
just = "center",
txt_gp = gpar(col = "white", cex = 1),
box_gp = gpar(fill = "white",
col = "white",
alpha = 0.01))
dchrg4
txt20 <- "49 (42.6%)"
txt21 <- "16 (13.9%)"
dchrg5 <- boxGrob(paste(c(txt14, txt20, txt16, txt21), collapse = "\n"),
x = coords(visit4_a)$right + unit(31, "mm"),
y = coords(visit2_a)$bottom - 1.7*distance(visit2_a,
visit2_a,
type = "h",
half = T),
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
dchrg5
# Connect the boxes and print/plot them
connectGrob(visit4_a, dchrg5, "L")
# 5. Updated flow analysis with dummy transparent boxGrob -----------------
grid.newpage()
txt1 <- "1,359 patients who attended PAC-19\n clinics from Aug-2020 to Jan-2023\n had their data entered in REDCap\n electronic database "
org_cohort <- boxGrob(txt1,
x = 0.5, y = .91,
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white", col = "black"))
org_cohort
txt2 <- "\n 1,359 (100%) PAC-19 clinic patients \n in REDCap electronic database"
xsec_study1 <- boxGrob(txt2,
x = 0.5,
y = coords(org_cohort)$bottom - distance(org_cohort,
org_cohort,
type = "h",
half = T) +
unit(5, "mm"),
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white", col = "black"))
xsec_study1
# Connect the boxes and print/plot them
connectGrob(org_cohort, xsec_study1, "vertical")
xsec_study2 <- boxGrob(expression(paste(bold("Cross-sectional analysis:"))),
x = 0.5,
y = coords(xsec_study1)$top - unit(5, "mm"),
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(col = "white", fill = "white", alpha = 0.1))
xsec_study2
txt3 <- "811 (59.7%) had only one \nPAC-19 clinic visit"
exclude_cohort <- boxGrob(txt3,
x = 0.8,
y = coords(xsec_study1)$top - distance(xsec_study1,
xsec_study1,
type = "h",
half = T) +
unit(5, "mm"),
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
exclude_cohort
# Connect the boxes and print/plot them
connectGrob(xsec_study1, exclude_cohort, "L")
long_study <- boxGrob(expression(paste(bold("Longitudinal analysis"))),
x = 0.5,
y = coords(exclude_cohort)$top - distance(exclude_cohort,
exclude_cohort,
type = "h",
half = T) -
unit(5, "mm"),
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(col = "white", fill = "white", alpha = 0.1))
long_study
# Connect the boxes and print/plot them
connectGrob(xsec_study1, long_study, "vertical")
txt4 <- "Visit 1:"
txt5 <- "548 (100%)"
visit1_a <- boxGrob(paste(c(txt4, txt5), collapse = "\n"),
x = 0.05,
y = coords(long_study)$bottom - 0.6*coords(long_study)$height,
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
# transparent dummy box
visit1_b <- boxGrob(paste(c(txt4, txt5), collapse = "\n"),
x = 0.05,
y = coords(visit1_a)$top + coords(visit1_a)$half_height,
just = "center",
txt_gp = gpar(col = "white", cex = 1),
box_gp = gpar(fill = "white",
col = "black", alpha = 0.01))
visit1_b
txt6 <- "Visit 5:"
txt7 <- "50 (43.5%)"
visit5 <- boxGrob(paste(c(txt6, txt7), collapse = "\n"),
x = 0.95,
y = coords(long_study)$bottom - 0.6*coords(long_study)$height,
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
txt8 <- "Visit 2:"
txt9 <- "548 (100%)"
visit2_a <- boxGrob(paste(c(txt8, txt9), collapse = "\n"),
x = coords(visit1_a)$right + 7.4*distance(visit1_a,
visit1_a,
type = "v",
half = T),
y = coords(long_study)$bottom - 0.6*coords(long_study)$height,
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
# transparent dummy box
visit2_b <- boxGrob(paste(c(txt4, txt5), collapse = "\n"),
x = coords(visit2_a)$right - coords(visit1_a)$half_width -
unit(4.5, "mm"),
y = coords(visit1_a)$top + coords(visit1_a)$half_height,
just = "center",
txt_gp = gpar(col = "white", cex = 1),
box_gp = gpar(fill = "white",
col = "white",
alpha = 0.01))
visit2_b
# transparent dummy box
visit2_c <- boxGrob(paste(c(txt4, txt5), collapse = "\n"),
x = coords(visit2_a)$right - coords(visit1_a)$half_width -
unit(4.5, "mm"),
y = coords(visit1_a)$top - coords(visit1_a)$half_height,
just = "center",
txt_gp = gpar(col = "white", cex = 1),
box_gp = gpar(fill = "white",
col = "white",
alpha = 0.01))
visit2_c
#
# Connect the boxes and print/plot them
connectGrob(visit1_b, visit2_c, "L")
txt10 <- "Visit 3:"
txt11 <- "234 (42.7%)"
visit3_a <- boxGrob(paste(c(txt10, txt11), collapse = "\n"),
x = 0.5,
y = coords(long_study)$bottom - 0.6*coords(long_study)$height,
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
# transparent dummy box
visit3_b <- boxGrob(paste(c(txt10, txt11), collapse = "\n"),
x = coords(visit3_a)$right - coords(visit3_a)$half_width -
unit(1.5, "mm"),
y = coords(visit3_a)$top + coords(visit3_a)$half_height,
just = "center",
txt_gp = gpar(col = "white", cex = 1),
box_gp = gpar(fill = "white",
col = "white",
alpha = 0.01
))
visit3_b
long_study
# Connect the boxes and print/plot them
connectGrob(xsec_study1, long_study, "vertical")
# transparent dummy box
visit3_c <- boxGrob(paste(c(txt10, txt11), collapse = "\n"),
x = coords(visit3_a)$right - 1.5*coords(visit3_a)$width -
unit(1.5, "mm"),
y = coords(visit3_a)$top - coords(visit3_a)$half_height,
just = "center",
txt_gp = gpar(col = "white", cex = 1),
box_gp = gpar(fill = "white",
col = "white",
alpha = 0.01
))
visit3_c
# Connect the boxes and print/plot them
connectGrob(visit2_b, visit3_c, "L")
txt12 <- "Visit 4:"
txt13 <- "115 (49.1%)"
visit4_a <- boxGrob(paste(c(txt12, txt13), collapse = "\n"),
x = 0.7,
y = coords(long_study)$bottom - 0.6*coords(long_study)$height,
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
# transparent dummy box
visit4_b <- boxGrob(paste(c(txt12, txt13), collapse = "\n"),
x = coords(visit4_a)$right - 0.5*coords(visit4_a)$half_width +
unit(2, "mm"),
y = coords(visit4_a)$top + coords(visit4_a)$half_height,
just = "center",
txt_gp = gpar(col = "white", cex = 1),
box_gp = gpar(fill = "white",
col = "white",
alpha = 0.01))
visit4_b
# transparent dummy box
visit4_c <- boxGrob(paste(c(txt12, txt13), collapse = "\n"),
x = coords(visit4_a)$right - 1.18*coords(visit4_a)$width,
y = coords(visit4_a)$top - coords(visit4_a)$half_height,
just = "center",
txt_gp = gpar(col = "white", cex = 1),
box_gp = gpar(fill = "white",
col = "white",
alpha = 0.01
))
visit4_c
# Connect the boxes and print/plot them
connectGrob(visit3_b, visit4_c, "L")
# Connect the boxes and print/plot them
connectGrob(visit4_b, visit5, "L")
visit1_a
visit5
alignVertical(reference = visit1_a,
visit2_a, visit3_a, visit4_a,
.position = "top") %>%
spreadHorizontal(.from = visit1_a,
.to = visit5)
txt14 <- "Discharged"
txt15 <- "216 (39.4%)"
txt16 <- "Lost to follow up"
txt17 <- "98 (17.9%)"
dchrg1 <- boxGrob(paste(c(txt14, txt15, txt16, txt17), collapse = "\n"),
x = coords(visit2_a)$right + unit(20, "mm"),
y = coords(visit2_a)$bottom - 1.7*distance(visit2_a,
visit2_a,
type = "h",
half = T),
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
dchrg1
# transparent dummy box
dchrg2 <- boxGrob(paste(c(txt14)),
x = coords(visit2_a)$right + unit(20, "mm"),
y = coords(visit2_a)$top - unit(3.1, "mm"),
just = "center",
txt_gp = gpar(col = "white", cex = 1),
box_gp = gpar(fill = "white",
col = "white",
alpha = 0.01))
dchrg2
# Connect the boxes and print/plot them
connectGrob(dchrg2, dchrg1, "vertical")
txt18 <- "78 (33.3%)"
txt19 <- "41 (17.6%)"
dchrg3 <- boxGrob(paste(c(txt14, txt18, txt16, txt19), collapse = "\n"),
x = coords(visit3_a)$right + unit(20, "mm"),
y = coords(visit2_a)$bottom - 1.7*distance(visit2_a,
visit2_a,
type = "h",
half = T),
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
dchrg3
# transparent dummy box
dchrg4 <- boxGrob(paste(c(txt14)),
x = coords(visit3_a)$right + unit(20, "mm"),
y = coords(visit3_a)$top - unit(3.1, "mm"),
just = "center",
txt_gp = gpar(col = "white", cex = 1),
box_gp = gpar(fill = "white",
col = "white",
alpha = 0.01))
dchrg4
# Connect the boxes and print/plot them
connectGrob(dchrg4, dchrg3, "vertical")
txt20 <- "49 (42.6%)"
txt21 <- "16 (13.9%)"
dchrg5 <- boxGrob(paste(c(txt14, txt20, txt16, txt21), collapse = "\n"),
x = coords(visit4_a)$right + unit(31, "mm"),
y = coords(visit2_a)$bottom - 1.7*distance(visit2_a,
visit2_a,
type = "h",
half = T),
just = "center",
txt_gp = gpar(col = "black", cex = 1),
box_gp = gpar(fill = "white",
col = "black"))
dchrg5
# transparent dummy box
dchrg6 <- boxGrob(paste(c(txt14)),
x = coords(visit4_a)$right + unit(31, "mm"),
y = coords(visit4_a)$top - unit(3.1, "mm"),
just = "center",
txt_gp = gpar(col = "white", cex = 1),
box_gp = gpar(fill = "white",
col = "white",
alpha = 0.01))
dchrg6
# Connect the boxes and print/plot them
connectGrob(dchrg6, dchrg5, "vertical")Thanks
Warren