R/finalGraphCreation.R
In GeraldCNelson/nutmod: Calculates nutrient information worldwide
Defines functions
layoutPlots
#' @author Gerald C. Nelson, \email{nelson.gerald.c@@gmail.com}
#' @keywords final graphs
#' @title Calculate final graph combinations for the nutrient modeling paper
#' @name finalGraphCreation.R
#' @description {
#' This code writes out pdfs of the graphs used in the final nutrient modeling paper.
#' The code grabs the individual graphs created in aggRun.R and places them in pdf file to be incorporated into the final word doc. There are 1 to 6
#' individual graphs per pdf. The layout is guided by the layoutMatrixx structure, where the last x is replaced by a number (1 to 6). The heightsx variables
#' control how tall the graph is in inches. The width is determined by the height variable and the relative width from the original file.
#' }
#Copyright (C) 2015-2017 Gerald C. Nelson, except where noted
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE, See the
# GNU General Public License for more details at http://www.gnu.org/licenses/.
source("R/nutrientModFunctions.R")
source("R/aggNorder.R")
library(grid)
# Cairo may be necessary for Calibri font
library(Cairo)
# extrafont may be necessary for Calibri font
library(extrafont)
# use staplr to merge pdfs and other manipulation
library(staplr)
sourceFile <- "finalGraphCreation.R"
description <- "This code writes out pdfs of the graphs used in the final nutrient modeling paper. The code grabs the individual graphs created in aggRun.R and places them in pdf file to be incorporated into the final word doc. There are 1 to 6 individual graphs per pdf. The layout is guided by the layoutMatrixx structure, where the last x is replaced by a number (1 to 6). The heightsx variables control how tall the graph is in inches. The width is determined by the height variable and the relative width from the original file."
gdxChoice <- "SSPs"
# delete all files in gDir/final - Commmented out but code left for future use
# graphicsPath <- paste(fileloc("gDir"), "final", sep = "/")
# graphicsFileList <- list.files(graphicsPath, all.files = TRUE)
# graphicsFileList <- paste(graphicsPath, graphicsFileList, sep = "/")
# invisible(unlink(graphicsFileList, recursive = FALSE))
# choose png or pdf output here.
fileouttype.device = cairo_pdf
fileouttype <- "pdf"
suffix = "var"
pdfDimensions <- data.table(fileName = character(0), height = character(0), width = character(0))
layoutPlots <- function(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths) {
cat("\n", figchoice, "figures:", get(figchoice))
plotNameList <- paste(prefix, "_", get(figchoice), sep = "")
plotNumberList <- which(graphNames %in% plotNameList)
cat("\nlayoutPlots plotNumberList:", plotNumberList)
plotNumberList <- c(plotNumberList, legendNum)
g.out <- grid.arrange(
grobs = graphsListHolder[plotNumberList],
ncol = colNum2, nrow = rowNum,
layout_matrix = layout,
widths = colWidths, heights = colHeights
)
ggsave(file = fileName,
plot = g.out,
device = fileouttype.device,
width = sum(colWidths), height = sum(colHeights) + 1) # +1 added to make bottom of the legend grob clear Nov 4, 2018
embed_fonts(fileName, outfile=fileName)
cat("\n", fileName)
pdfDimensions <- as.list(c(fileName, sum(colHeights), sum(colWidths)))
return(pdfDimensions)
}
# prefix defined here
prefix <- "SSPs_scenOrderSSP"
scenChoiceList <- "scenOrderSSP"
colNum2 <- 2 # how many columns of graphs per page
colWidths1 <- c(7) # how wide the column are
colWidths2 <- c(2.9, 2.9) # how wide the 2 columns are
layoutMatrix6 <- rbind(c(1, 2), c(3, 4), c(5, 6), c(7)) # the order in which the graphs are placed on the page. The 7th graph is the legend.
layoutMatrix5 <- rbind(c(1, 2), c(3, 4), c(5, 6))
layoutMatrix4 <- rbind(c(1, 2), c(3, 4), c(5))
layoutMatrix3 <- rbind(c(1, 2), c(3, 4))
layoutMatrix2 <- rbind(c(1, 2), c(3))
layoutMatrix1 <- rbind(c(1), c(2))
heights6 <- c(2.75, 2.75, 2.75, 0.2)
heights5 <- c(2.9, 2.9, 2.9)
heights4 <- c(2.9, 2.9, 0.2)
heights3 <- c(2.9, 2.9)
heights2 <- c(2.9, 0.2)
heights1 <- c(4, 0.2)
#' starting names list
macroList <- c("carbohydrate_g", "protein_g", "fat_g", "totalfiber_g")
minrlsList <- c("calcium_mg", "iron_mg", "magnesium_mg", "phosphorus_mg", "potassium_g", "zinc_mg")
vitsList <- c("folate_µg", "niacin_mg", "riboflavin_mg",
"thiamin_mg", "vit_a_rae_µg", "vit_b6_mg",
"vit_b12_µg", "vit_c_mg", "vit_d_µg", "vit_e_mg", "vit_k_µg")
macroList.reqRatio <- paste(prefix, macroList[!macroList %in% "fat_g"], ".reqRatio", sep = "")
macroList.AMDR <- macroList[!macroList %in% "totalfiber_g"]
# figS definitions are below. Some combine different aggregation choices. All use the different suffixes.
gc(verbose = FALSE) # garbage collection Not sure this makes any difference
# get the file that holds all the graphs produced for suffix
newFile <- paste("graphsListHolder", suffix, sep = ".")
graphsListHolder <- getNewestVersion(fileShortName = newFile, directory = fileloc("gDir"), fileType = "rds")
finalDir <- paste0(fileloc("gDir"),"/final/")
createMissingDir(finalDir) # checks for the existence of the directory and if its not available, creates it. Dec 21, 2018
# get the names of all the graphs in the graphsListerHolder file
graphNames <- names(graphsListHolder)
legendHorizontal <- paste("legend", "bottom", gdxChoice, scenChoiceList, "WB", sep = "_") # using WB instead of aggChoice because WB and tenregion legends are the same
legendVertical <- paste("legend", "right", gdxChoice, scenChoiceList, "WB", sep = "_")
legendHorizontalNum <- which(graphNames %in% legendHorizontal)
legendVerticalNum <- which(graphNames %in% legendVertical)
#' figS that combine a single plot from two regions - WB and tenregions -----
# includes WB on left and tenregion on right
figS6.nutavail.zinc <- paste(c("nutrients.avail_zinc_mg"), sep = "_") # leave suffix out of this code
for (figchoice in c("figS6.nutavail.zinc")) {
rowNum <- 2
legendNum <- legendHorizontalNum
layout <- layoutMatrix2
colWidths <- colWidths2
colHeights <- heights2
plotNameList <- paste(prefix, "_", get(figchoice), "_", "WB", ".", suffix, sep = "")
plotNameList <- c(plotNameList, paste(prefix, "_", get(figchoice), "_", "tenregions", ".", suffix, sep = ""))
#' rev here reverses the order in which the graphs are plotted. removed July 12, 2018
plotNumberList <- which(graphNames %in% plotNameList)
fileName <- paste(finalDir, figchoice, ".", suffix, ".", fileouttype, sep = "")
cat("\nfigS6.nutavail.zinc plotNumberList:", plotNumberList, "\n")
plotNumberList <- c(plotNumberList, legendNum)
g.out <- grid.arrange(
grobs = graphsListHolder[plotNumberList],
ncol = colNum2, nrow = rowNum,
layout_matrix = layout,
widths = colWidths, heights = colHeights
)
fileName <- paste(finalDir, figchoice, ".", suffix, ".", fileouttype, sep = "")
fileDims <- as.list(c(fileName, sum(colHeights), sum(colWidths)))
ggsave(file = fileName, plot = g.out, width = sum(colWidths), height = sum(colHeights) +1, device = fileouttype.device)
embed_fonts(fileName, outfile=fileName)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
fig3.facetMapRR_2010 <- paste("facetmap_nutReqRatio_2010", suffix, sep = ".")
fig4.facetMapRR_IncDelta <- paste("facetmap_nutReqRatioChange_income", suffix, sep = ".")
fig5.facetMapRR_CCDelta <- paste("facetmap_nutReqRatioChange_climate", suffix, sep = ".")
# facetMapRR_2050NoCC <- paste("facetmap_nutReqRatio_2050_NoCC", suffix, sep = ".")
figS1.facetMapBudgetShare2010_50 <- paste("facetmap_budgetShare_2010_50_SSP2_HGEM.world", sep = ".")
figS10.1.facetMapMRV_2010 <- paste("facetmap_MRVRatio_2010", suffix, sep = ".")
figS10.2.facetMapMRV_IncDelta <- paste("facetmap_MRVRatioChange_income", suffix, sep = ".")
figS10.3.facetMapMRV_CCDelta <- paste("facetmap_MRVRatioChange_climate", suffix, sep = ".")
# plot facet maps
# special handling of files not created in aggrun.R for SSPs
fileListOld <- c("SSPs_scenOrderSSP_CGEeffects.png", "SSPs_scenOrderSSP_facetmap_macroMetrics_2050.png")
fileListNew <- c("Figures2.png", "Figures3.png")
oldDir = paste(getwd(), "graphics", gdxChoice, sep = "/")
newDir = paste(getwd(), "graphics", gdxChoice, "final", sep = "/")
for (i in 1:length(fileListOld)) {
file.copy(paste(oldDir, fileListOld[i], sep = "/"), newDir, overwrite = TRUE)
file.rename(paste(newDir, fileListOld[i], sep = "/"), (paste(newDir, fileListNew[i], sep = "/")))
cat("dest:", paste(newDir, fileListNew[i], sep = "/"), "\n")
}
# end special handling
# facet map graphs -----
for (figchoice in c("fig5.facetMapRR_CCDelta", "fig4.facetMapRR_IncDelta", "fig3.facetMapRR_2010", "figS1.facetMapBudgetShare2010_50",
"figS10.1.facetMapMRV_2010", "figS10.2.facetMapMRV_IncDelta","figS10.3.facetMapMRV_CCDelta")) {
plotNameList <- paste(prefix, "_", get(figchoice), sep = "")
cat(plotNameList)
plotNumberList <- which(graphNames %in% plotNameList)
cat("\nSSPs facet plotNumberList:", plotNumberList, "\n")
fileName <- paste(finalDir, figchoice, ".", suffix, ".", fileouttype, sep = "")
colWidths <- 7
colHeights <- 4
g.out <- grid.arrange(
grobs = graphsListHolder[plotNumberList],
ncol = 1, nrow = 1,
layout_matrix = layout,
widths = colWidths, heights = colHeights
)
# ggsave(file = fileName, plot = graphsListHolder[[plotNumberList]], width = colWidths, height = colHeights)
ggsave(file = fileName, plot = g.out, width = sum(colWidths), height = sum(colHeights) +1, device = fileouttype.device, dpi = 300)
embed_fonts(fileName, outfile=fileName)
fileDims <- as.list(c(fileName, sum(colHeights), sum(colWidths)))
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
# The following code seems a duplicate of the code just above it so commenting out. Dec 21, 2018
# for (figchoice in c( "fig4.facetMapRR_IncDelta", "fig3.facetMapRR_2010",
# "figS10.1.facetMapMRV_2010", "figS10.2.facetMapMRV_IncDelta")) {
# plotNameList <- paste(prefix, "_", get(figchoice), sep = "")
# plotNumberList <- which(graphNames %in% plotNameList)
# cat("\facet plotNumberList:", plotNumberList, "\n")
# fileName <- paste(finalDir, figchoice, ".", suffix, ".", fileouttype, sep = "")
# colWidths <- 7
# colHeights <- 6
# g.out <- grid.arrange(
# grobs = graphsListHolder[plotNumberList],
# ncol = 1, nrow = 1,
# layout_matrix = layout,
# widths = colWidths, heights = colHeights
# )
# ggsave(file = fileName, plot = g.out, width = sum(colWidths), height = sum(colHeights) +1, device = fileouttype.device)
# embed_fonts(fileName, outfile=fileName)
# fileDims <- as.list(c(fileName, sum(colHeights), sum(colWidths)))
# pdfDimensions <- rbind(pdfDimensions, fileDims)
# }
#' Fig 1 budget, combines bar charts and box plots; box plots not for tenregions -----
fig1.budgetShare <- paste(c("budgetShare", "budgetShareBoxPlot_2050"), "_", "WB", ".", suffix, sep = "")
for (figchoice in c("fig1.budgetShare")) {
rowNum <- 2
legendNum <- legendHorizontalNum
layout <- layoutMatrix2
colWidths <- colWidths2
colHeights <-heights2
fileName <- paste(finalDir, figchoice, "_", aggChoice = "WB", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
#' Fig S4 availability -----
#' foodgroup availability ratio part 1 - 6 graphs
figS4.foodavail.1 <- paste(c("foodAvail_foodGroup_alcohol", "foodAvail_foodGroup_beverages",
"foodAvail_foodGroup_cereals", "foodAvail_foodGroup_dairy",
"foodAvail_foodGroup_eggs", "foodAvail_foodGroup_fish"), "_", "WB", ".", suffix, sep = "")
#' foodgroup availability part 2 - 6 graphs
figS4.foodavail.2 <- paste(c("foodAvail_foodGroup_fruits", "foodAvail_foodGroup_meats",
"foodAvail_foodGroup_nutsNseeds", "foodAvail_foodGroup_oils",
"foodAvail_foodGroup_pulses", "foodAvail_foodGroup_rootsNPlantain"), "_", "WB", ".", suffix, sep = "")
#' foodgroup availability", part 3 - 2 graphs
figS4.foodavail.3 <- paste(c("foodAvail_foodGroup_sweeteners", "foodAvail_foodGroup_vegetables"), "_", "WB", ".", suffix, sep = "")
#' Fig 2 micronutrients adequacy ratio ------
#' micronutrients adequacy", "part 2 and 3 vitamins
figS7.2.adequacy.vits_1<- paste(c("reqRatio_vits_folate_µg", "reqRatio_vits_niacin_mg",
"reqRatio_vits_riboflavin_mg", "reqRatio_vits_thiamin_mg",
"reqRatio_vits_vit_a_rae_µg", "reqRatio_vits_vit_b6_mg"), "_", "WB", ".", suffix, sep = "")
figS7.2.adequacy.vits_2 <- paste(c("reqRatio_vits_vit_b12_µg", "reqRatio_vits_vit_c_mg",
"reqRatio_vits_vit_d_µg", "reqRatio_vits_vit_e_mg",
"reqRatio_vits_vit_k_µg"), "_", "WB", ".", suffix, sep = "")
# vits candidates for removal - niacin, thiamin, vitamin b6
#' micronutrients adequacy", "part 1 minerals
figS7.3.adequacy.minrls <- paste(c("reqRatio_minrls_calcium_mg", "reqRatio_minrls_iron_mg",
"reqRatio_minrls_magnesium_mg", "reqRatio_minrls_phosphorus_mg",
"reqRatio_minrls_potassium_g", "reqRatio_minrls_zinc_mg"), "_", "WB", ".", suffix, sep = "")
#' Fig S2 kcal availability - 1 graph
figS5.energyavail.WB <- paste(c("kcals.tot.perDay"), "_", "WB", ".", suffix, sep = "")
figS12.budgetShare <- paste(c("budgetShare"), "_", "tenregions", ".", suffix, sep = "")
figS14.energyavail.10regions <- paste(c("kcals.tot.perDay"), "_", "tenregions", ".", suffix, sep = "")
#' Fig s7.0 macro nutrients adequacy ratio, 3 plots per page
figS7.0.adequacy.macro <- paste(c("reqRatio_macro_carbohydrate_g", "reqRatio_macro_protein_g",
"reqRatio_macro_totalfiber_g"), "_", "WB", ".", suffix, sep = "")
#' #' Fig 2 minrl nutrients adequacy ratio, 6 plots per page
#' fig2.adequacy.minrls <- paste(c("minrls_calcium_mg", "minrls_iron_mg", "minrls_magnesium_mg", "minrls_phosphorus_mg",
#' "minrls_potassium_g", "minrls_zinc_mg"), "_", "WB", ".", suffix, sep = "")
#'
#' #' Fig 2 vits 1 nutrients adequacy ratio, 6 plots per page
#' fig2.adequacy.vits.1 <- paste(c("vits_folate_µg", "vits_niacin_mg", "vits_riboflavin_mg", "vits_thiamin_mg",
#' "vits_vit_a_rae_µg", "vits_vit_b6_mg" ), "_", "WB", ".", suffix, sep = "")
#'
#' #' Fig 2 vits 2 nutrients adequacy ratio, 5 plots per page
#' fig2.adequacy.vits. <- paste(c("vits_vit_b6_µg", "vits_vit_c_mg", "vits_vit_d_µg", "vits_vit_e_mg",
#' "vits_vit_k_µg"), "_", "WB", ".", suffix, sep = "")
#' Fig macro AMDRs ------, 3 plots per page
fig2.AMDRhiLo <- paste(c("AMDRShare_carbohydrate_g", "AMDRShare_protein_g",
"AMDRShare_fat_g"), "_", "WB", ".", suffix, sep = "")
figS16.AMDRhiLo <- paste(c("AMDRShare_carbohydrate_g", "AMDRShare_protein_g",
"AMDRShare_fat_g"), "_", "tenregions", ".", suffix, sep = "")
# minrls candidates for removal - magnesium, phosphorus
#' Fig 5 composite DI and nutrient balance ------
figS8.compDINB <- paste(c("compDI", "NutBalScore"), "_", "WB", ".", suffix, sep = "")
figS18.compDINB <- paste(c("compDI", "NutBalScore"), "_", "tenregions", ".", suffix, sep = "")
#' figS8 x Rao and nonstaple share ------
figS8.RaoNenergyShareNonStaples <- paste(c("nonStapleShare", "RAOqe"), "_", "WB", ".", suffix, sep = "")
#' figSS6. Ratio of disqualifying nutrient to its MRV
figS11.badRatios <- paste(c("badRatios_ethanol_g", "badRatios_ft_acds_tot_sat_g", "badRatios_sugar_g"), "_", "WB", ".", suffix, sep = "")
#' Fig S8 availability -----
#' foodgroup availability ratio part 1 - 6 graphs
figS13.foodavail.1 <- paste(c("foodAvail_foodGroup_alcohol", "foodAvail_foodGroup_beverages",
"foodAvail_foodGroup_cereals", "foodAvail_foodGroup_dairy",
"foodAvail_foodGroup_eggs", "foodAvail_foodGroup_fish"), "_", "tenregions", ".", suffix, sep = "")
#' foodgroup availability part 2 - 6 graphs
figS13.foodavail.2 <- paste(c("foodAvail_foodGroup_fruits", "foodAvail_foodGroup_meats",
"foodAvail_foodGroup_nutsNseeds", "foodAvail_foodGroup_oils",
"foodAvail_foodGroup_pulses", "foodAvail_foodGroup_rootsNPlantain"), "_", "tenregions", ".", suffix, sep = "")
#' foodgroup availability", part 3 - 2 graphs
figS13.foodavail.3 <- paste(c("foodAvail_foodGroup_sweeteners", "foodAvail_foodGroup_vegetables"), "_", "tenregions", ".", suffix, sep = "")
#' Fig S17 tenregions micronutrients adequacy ratio ------
#' micronutrients adequacy", "part 2 and 3 vitamins
figS17.1.adequacy.vits <- paste(c("reqRatio_vits_folate_µg", "reqRatio_vits_niacin_mg",
"reqRatio_vits_riboflavin_mg", "reqRatio_vits_thiamin_mg",
"reqRatio_vits_vit_a_rae_µg", "reqRatio_vits_vit_b6_mg"), "_", "tenregions", ".", suffix, sep = "")
figS17.2.adequacy.vits <- paste(c("reqRatio_vits_vit_b12_µg", "reqRatio_vits_vit_c_mg",
"reqRatio_vits_vit_d_µg", "reqRatio_vits_vit_e_mg",
"reqRatio_vits_vit_k_µg"), "_", "tenregions", ".", suffix, sep = "")
# vits candidates for removal - niacin, thiamin, vitamin b6
#' micronutrients adequacy", "part 1 minerals
figS17.3.adequacy.minrls <- paste(c("reqRatio_minrls_calcium_mg", "reqRatio_minrls_iron_mg",
"reqRatio_minrls_magnesium_mg", "reqRatio_minrls_phosphorus_mg",
"reqRatio_minrls_potassium_g", "reqRatio_minrls_zinc_mg"), "_", "tenregions", ".", suffix, sep = "")
figS15.adequacy.macro <- paste(c("reqRatio_macro_carbohydrate_g", "reqRatio_macro_protein_g",
"reqRatio_macro_totalfiber_g"), "_", "tenregions", ".", suffix, sep = "")
#' figS with 6 plots -----
rowNum <- 4
legendNum <- legendHorizontalNum
layout <- layoutMatrix6
colWidths <- colWidths2
colHeights <-heights6
for (figchoice in c( "figS7.2.adequacy.vits_1", "figS7.3.adequacy.minrls" )) {
cat("\nfigchoice:", figchoice, "\n")
fileName <- paste(finalDir, figchoice, "_", "WB", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
for (figchoice in c("figS4.foodavail.1", "figS4.foodavail.2")) {
cat("\nfigchoice:", figchoice, "\n")
fileName <- paste(finalDir, figchoice, "_", "WB", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
for (figchoice in c( "figS13.foodavail.1", "figS13.foodavail.2", "figS17.1.adequacy.vits", "figS17.3.adequacy.minrls")) {
cat("\nfigchoice:", figchoice, "\n")
fileName <- paste(finalDir, figchoice, "_", "tenregions", ".", suffix, ".", fileouttype, sep = "")
cat("fileName: ", fileName, "\n")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
#' figS with 5 plots -----
for (figchoice in c("figS7.2.adequacy.vits_2")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 3
legendNum <- legendVerticalNum
layout <- layoutMatrix5
colWidths <- colWidths2
colHeights <-heights5
fileName <- paste(finalDir, figchoice, "_", "WB", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
for (figchoice in c("figS17.2.adequacy.vits")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 3
legendNum <- legendVerticalNum
layout <- layoutMatrix5
colWidths <- colWidths2
colHeights <-heights5
fileName <- paste(finalDir, figchoice, "_", "tenregions", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
#' figS with 1 plot and horizontal legend at bottom
for (figchoice in c("figS5.energyavail.WB")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 2
legendNum <- legendHorizontalNum
layout <- layoutMatrix1
colWidths <- 5.8
colHeights <- heights1
plotNameList <- paste(prefix, "_", get(figchoice), sep = "")
plotNumberList <- which(graphNames %in% plotNameList)
plotNumberList <- c(plotNumberList, legendNum)
g.out <- grid.arrange(
grobs = graphsListHolder[plotNumberList],
ncol = length(colWidths), nrow = rowNum,
layout_matrix = layout,
widths = colWidths, heights = colHeights
)
fileName <- paste(finalDir, figchoice, ".", suffix, ".", fileouttype, sep = "")
fileDims <- as.list(c(fileName, sum(colHeights), sum(colWidths)))
# ggsave(file = fileName, plot = g.out, width = sum(colWidths), height = sum(colHeights))
ggsave(file = fileName, plot = g.out, width = sum(colWidths), height = sum(colHeights) +1, device = fileouttype.device)
embed_fonts(fileName, outfile=fileName)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
for (figchoice in c("figS12.budgetShare")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 2
legendNum <- legendHorizontalNum
layout <- layoutMatrix1
colWidths <- 5.8
colHeights <- heights1
plotNameList <- paste(prefix, "_", get(figchoice), sep = "")
plotNumberList <- which(graphNames %in% plotNameList)
plotNumberList <- c(plotNumberList, legendNum)
g.out <- grid.arrange(
grobs = graphsListHolder[plotNumberList],
ncol = length(colWidths), nrow = rowNum,
layout_matrix = layout,
widths = colWidths, heights = colHeights
)
fileName <- paste(finalDir, figchoice, "_", aggChoice = "tenregions", ".", suffix, ".", fileouttype, sep = "")
fileDims <- as.list(c(fileName, sum(colHeights), sum(colWidths)))
ggsave(file = fileName, plot = g.out, width = sum(colWidths), height = sum(colHeights), device = fileouttype.device)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
for (figchoice in c("figS14.energyavail.10regions")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 2
legendNum <- legendHorizontalNum
layout <- layoutMatrix1
colWidths <- 5.8
colHeights <- heights1
plotNameList <- paste(prefix, "_", get(figchoice), sep = "")
plotNumberList <- which(graphNames %in% plotNameList)
plotNumberList <- c(plotNumberList, legendNum)
g.out <- grid.arrange(
grobs = graphsListHolder[plotNumberList],
ncol = length(colWidths), nrow = rowNum,
layout_matrix = layout,
widths = colWidths, heights = colHeights
)
fileName <- paste(finalDir, figchoice, "_", aggChoice = "tenregions", ".", suffix, ".", fileouttype, sep = "")
fileDims <- as.list(c(fileName, sum(colHeights), sum(colWidths)))
# ggsave(file = fileName, plot = g.out, width = sum(colWidths), height = sum(colHeights))
ggsave(file = fileName, plot = g.out, width = sum(colWidths), height = sum(colHeights) +1, device = fileouttype.device)
embed_fonts(fileName, outfile=fileName)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
#' figS with 2 plots -----
for (figchoice in c("figS4.foodavail.3", "figS8.compDINB", "figS8.RaoNenergyShareNonStaples")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 2
legendNum <- legendHorizontalNum
layout <- layoutMatrix2
colWidths <- colWidths2
colHeights <-heights2
fileName <- paste(finalDir, figchoice, "_", "WB", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
for (figchoice in c("figS13.foodavail.3", "figS18.compDINB")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 2
legendNum <- legendHorizontalNum
layout <- layoutMatrix2
colWidths <- colWidths2
colHeights <-heights2
fileName <- paste(finalDir, figchoice, "_", "tenregions", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
#' figS with 3 plots -----
for (figchoice in c("fig2.AMDRhiLo", "figS7.0.adequacy.macro", "figS11.badRatios")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 2
legendNum <- legendVerticalNum
layout <- layoutMatrix3
colWidths <- colWidths2
colHeights <-heights3
fileName <- paste(finalDir, figchoice, "_", "WB", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
for (figchoice in c("figS15.adequacy.macro", "figS16.AMDRhiLo")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 2
legendNum <- legendVerticalNum
layout <- layoutMatrix3
colWidths <- colWidths2
colHeights <-heights3
fileName <- paste(finalDir, figchoice, "_", "tenregions", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
# } commented out switchloop Nov 15.
dt.finalGraphicsNames <- as.data.table(read_csv("data-raw/finalGraphicsNames.csv"), col_names = TRUE)
for (i in 1:nrow(dt.finalGraphicsNames)){
fileFrom <- paste0(fileloc("gDir"), "/final/", dt.finalGraphicsNames$X1[i])
fileTo <- paste0(fileloc("gDir"), "/final/", dt.finalGraphicsNames$X2[i])
file.rename(fileFrom, fileTo)
}
# combine selected pdfs using staple_pdf from package staplr
# fig2list.in <- c("figure2.0.pdf", "figure2.1.pdf", "figure2.2.pdf", "figure2.3.pdf")
# fig2list.out <- "figure2.pdf"
figS4list.in <- c("figureS4.1.pdf", "figureS4.2.pdf", "figureS4.3.pdf")
figS4list.out <- "figureS4.pdf"
figS10list.in <- c("figureS10.1.pdf", "figureS10.2.pdf", "figureS10.3.pdf")
figS10list.out <- "figureS10.pdf"
figS13list.in <- c("figures13.1.pdf", "figures13.2.pdf", "figures13.3.pdf")
figS13list.out <- "figures13.pdf"
figS17list.in <- c("figures17.1.pdf", "figures17.2.pdf", "figures17.3.pdf")
figS17list.out <- "figures17.pdf"
input_directory <- paste0(fileloc("gDir"), "/final")
lists <- c("figS4", "figS9", "figS13", "figS17")
# create one pdf out of several
for (i in 1:length(lists)){
list.in <- get(paste0(lists[i], "list.in"))
list.out <- get(paste0(lists[i], "list.out"))
input_directory <- paste0(fileloc("gDir"), "/final")
output_filepath <- paste(input_directory, list.out, sep = "/")
staple_pdf(input_files = paste(input_directory, list.in, sep = "/"),
output_filepath = output_filepath)
}
createScriptMetaData()
inDT <- pdfDimensions
outName <- "pdfDimensions"
desc <- "final graph file name, height and width"
cleanup(inDT, outName, fileloc("gDir"), desc = desc)
# how to get rid of x axis labels for the first graph in listHolder
# temp <- graphsListHolder[[1]]
# temp + theme(axis.title.x=element_blank(),
# + axis.text.x=element_blank(),
# + axis.ticks.x=element_blank())
GeraldCNelson/nutmod documentation built on May 8, 2023, 8:04 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions layoutPlots
#' @author Gerald C. Nelson, \email{nelson.gerald.c@@gmail.com}
#' @keywords final graphs
#' @title Calculate final graph combinations for the nutrient modeling paper
#' @name finalGraphCreation.R
#' @description {
#' This code writes out pdfs of the graphs used in the final nutrient modeling paper.
#' The code grabs the individual graphs created in aggRun.R and places them in pdf file to be incorporated into the final word doc. There are 1 to 6
#' individual graphs per pdf. The layout is guided by the layoutMatrixx structure, where the last x is replaced by a number (1 to 6). The heightsx variables
#' control how tall the graph is in inches. The width is determined by the height variable and the relative width from the original file.
#' }
#Copyright (C) 2015-2017 Gerald C. Nelson, except where noted
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE, See the
# GNU General Public License for more details at http://www.gnu.org/licenses/.
source("R/nutrientModFunctions.R")
source("R/aggNorder.R")
library(grid)
# Cairo may be necessary for Calibri font
library(Cairo)
# extrafont may be necessary for Calibri font
library(extrafont)
# use staplr to merge pdfs and other manipulation
library(staplr)
sourceFile <- "finalGraphCreation.R"
description <- "This code writes out pdfs of the graphs used in the final nutrient modeling paper. The code grabs the individual graphs created in aggRun.R and places them in pdf file to be incorporated into the final word doc. There are 1 to 6 individual graphs per pdf. The layout is guided by the layoutMatrixx structure, where the last x is replaced by a number (1 to 6). The heightsx variables control how tall the graph is in inches. The width is determined by the height variable and the relative width from the original file."
gdxChoice <- "SSPs"
# delete all files in gDir/final - Commmented out but code left for future use
# graphicsPath <- paste(fileloc("gDir"), "final", sep = "/")
# graphicsFileList <- list.files(graphicsPath, all.files = TRUE)
# graphicsFileList <- paste(graphicsPath, graphicsFileList, sep = "/")
# invisible(unlink(graphicsFileList, recursive = FALSE))
# choose png or pdf output here.
fileouttype.device = cairo_pdf
fileouttype <- "pdf"
suffix = "var"
pdfDimensions <- data.table(fileName = character(0), height = character(0), width = character(0))
layoutPlots <- function(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths) {
cat("\n", figchoice, "figures:", get(figchoice))
plotNameList <- paste(prefix, "_", get(figchoice), sep = "")
plotNumberList <- which(graphNames %in% plotNameList)
cat("\nlayoutPlots plotNumberList:", plotNumberList)
plotNumberList <- c(plotNumberList, legendNum)
g.out <- grid.arrange(
grobs = graphsListHolder[plotNumberList],
ncol = colNum2, nrow = rowNum,
layout_matrix = layout,
widths = colWidths, heights = colHeights
)
ggsave(file = fileName,
plot = g.out,
device = fileouttype.device,
width = sum(colWidths), height = sum(colHeights) + 1) # +1 added to make bottom of the legend grob clear Nov 4, 2018
embed_fonts(fileName, outfile=fileName)
cat("\n", fileName)
pdfDimensions <- as.list(c(fileName, sum(colHeights), sum(colWidths)))
return(pdfDimensions)
}
# prefix defined here
prefix <- "SSPs_scenOrderSSP"
scenChoiceList <- "scenOrderSSP"
colNum2 <- 2 # how many columns of graphs per page
colWidths1 <- c(7) # how wide the column are
colWidths2 <- c(2.9, 2.9) # how wide the 2 columns are
layoutMatrix6 <- rbind(c(1, 2), c(3, 4), c(5, 6), c(7)) # the order in which the graphs are placed on the page. The 7th graph is the legend.
layoutMatrix5 <- rbind(c(1, 2), c(3, 4), c(5, 6))
layoutMatrix4 <- rbind(c(1, 2), c(3, 4), c(5))
layoutMatrix3 <- rbind(c(1, 2), c(3, 4))
layoutMatrix2 <- rbind(c(1, 2), c(3))
layoutMatrix1 <- rbind(c(1), c(2))
heights6 <- c(2.75, 2.75, 2.75, 0.2)
heights5 <- c(2.9, 2.9, 2.9)
heights4 <- c(2.9, 2.9, 0.2)
heights3 <- c(2.9, 2.9)
heights2 <- c(2.9, 0.2)
heights1 <- c(4, 0.2)
#' starting names list
macroList <- c("carbohydrate_g", "protein_g", "fat_g", "totalfiber_g")
minrlsList <- c("calcium_mg", "iron_mg", "magnesium_mg", "phosphorus_mg", "potassium_g", "zinc_mg")
vitsList <- c("folate_µg", "niacin_mg", "riboflavin_mg",
"thiamin_mg", "vit_a_rae_µg", "vit_b6_mg",
"vit_b12_µg", "vit_c_mg", "vit_d_µg", "vit_e_mg", "vit_k_µg")
macroList.reqRatio <- paste(prefix, macroList[!macroList %in% "fat_g"], ".reqRatio", sep = "")
macroList.AMDR <- macroList[!macroList %in% "totalfiber_g"]
# figS definitions are below. Some combine different aggregation choices. All use the different suffixes.
gc(verbose = FALSE) # garbage collection Not sure this makes any difference
# get the file that holds all the graphs produced for suffix
newFile <- paste("graphsListHolder", suffix, sep = ".")
graphsListHolder <- getNewestVersion(fileShortName = newFile, directory = fileloc("gDir"), fileType = "rds")
finalDir <- paste0(fileloc("gDir"),"/final/")
createMissingDir(finalDir) # checks for the existence of the directory and if its not available, creates it. Dec 21, 2018
# get the names of all the graphs in the graphsListerHolder file
graphNames <- names(graphsListHolder)
legendHorizontal <- paste("legend", "bottom", gdxChoice, scenChoiceList, "WB", sep = "_") # using WB instead of aggChoice because WB and tenregion legends are the same
legendVertical <- paste("legend", "right", gdxChoice, scenChoiceList, "WB", sep = "_")
legendHorizontalNum <- which(graphNames %in% legendHorizontal)
legendVerticalNum <- which(graphNames %in% legendVertical)
#' figS that combine a single plot from two regions - WB and tenregions -----
# includes WB on left and tenregion on right
figS6.nutavail.zinc <- paste(c("nutrients.avail_zinc_mg"), sep = "_") # leave suffix out of this code
for (figchoice in c("figS6.nutavail.zinc")) {
rowNum <- 2
legendNum <- legendHorizontalNum
layout <- layoutMatrix2
colWidths <- colWidths2
colHeights <- heights2
plotNameList <- paste(prefix, "_", get(figchoice), "_", "WB", ".", suffix, sep = "")
plotNameList <- c(plotNameList, paste(prefix, "_", get(figchoice), "_", "tenregions", ".", suffix, sep = ""))
#' rev here reverses the order in which the graphs are plotted. removed July 12, 2018
plotNumberList <- which(graphNames %in% plotNameList)
fileName <- paste(finalDir, figchoice, ".", suffix, ".", fileouttype, sep = "")
cat("\nfigS6.nutavail.zinc plotNumberList:", plotNumberList, "\n")
plotNumberList <- c(plotNumberList, legendNum)
g.out <- grid.arrange(
grobs = graphsListHolder[plotNumberList],
ncol = colNum2, nrow = rowNum,
layout_matrix = layout,
widths = colWidths, heights = colHeights
)
fileName <- paste(finalDir, figchoice, ".", suffix, ".", fileouttype, sep = "")
fileDims <- as.list(c(fileName, sum(colHeights), sum(colWidths)))
ggsave(file = fileName, plot = g.out, width = sum(colWidths), height = sum(colHeights) +1, device = fileouttype.device)
embed_fonts(fileName, outfile=fileName)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
fig3.facetMapRR_2010 <- paste("facetmap_nutReqRatio_2010", suffix, sep = ".")
fig4.facetMapRR_IncDelta <- paste("facetmap_nutReqRatioChange_income", suffix, sep = ".")
fig5.facetMapRR_CCDelta <- paste("facetmap_nutReqRatioChange_climate", suffix, sep = ".")
# facetMapRR_2050NoCC <- paste("facetmap_nutReqRatio_2050_NoCC", suffix, sep = ".")
figS1.facetMapBudgetShare2010_50 <- paste("facetmap_budgetShare_2010_50_SSP2_HGEM.world", sep = ".")
figS10.1.facetMapMRV_2010 <- paste("facetmap_MRVRatio_2010", suffix, sep = ".")
figS10.2.facetMapMRV_IncDelta <- paste("facetmap_MRVRatioChange_income", suffix, sep = ".")
figS10.3.facetMapMRV_CCDelta <- paste("facetmap_MRVRatioChange_climate", suffix, sep = ".")
# plot facet maps
# special handling of files not created in aggrun.R for SSPs
fileListOld <- c("SSPs_scenOrderSSP_CGEeffects.png", "SSPs_scenOrderSSP_facetmap_macroMetrics_2050.png")
fileListNew <- c("Figures2.png", "Figures3.png")
oldDir = paste(getwd(), "graphics", gdxChoice, sep = "/")
newDir = paste(getwd(), "graphics", gdxChoice, "final", sep = "/")
for (i in 1:length(fileListOld)) {
file.copy(paste(oldDir, fileListOld[i], sep = "/"), newDir, overwrite = TRUE)
file.rename(paste(newDir, fileListOld[i], sep = "/"), (paste(newDir, fileListNew[i], sep = "/")))
cat("dest:", paste(newDir, fileListNew[i], sep = "/"), "\n")
}
# end special handling
# facet map graphs -----
for (figchoice in c("fig5.facetMapRR_CCDelta", "fig4.facetMapRR_IncDelta", "fig3.facetMapRR_2010", "figS1.facetMapBudgetShare2010_50",
"figS10.1.facetMapMRV_2010", "figS10.2.facetMapMRV_IncDelta","figS10.3.facetMapMRV_CCDelta")) {
plotNameList <- paste(prefix, "_", get(figchoice), sep = "")
cat(plotNameList)
plotNumberList <- which(graphNames %in% plotNameList)
cat("\nSSPs facet plotNumberList:", plotNumberList, "\n")
fileName <- paste(finalDir, figchoice, ".", suffix, ".", fileouttype, sep = "")
colWidths <- 7
colHeights <- 4
g.out <- grid.arrange(
grobs = graphsListHolder[plotNumberList],
ncol = 1, nrow = 1,
layout_matrix = layout,
widths = colWidths, heights = colHeights
)
# ggsave(file = fileName, plot = graphsListHolder[[plotNumberList]], width = colWidths, height = colHeights)
ggsave(file = fileName, plot = g.out, width = sum(colWidths), height = sum(colHeights) +1, device = fileouttype.device, dpi = 300)
embed_fonts(fileName, outfile=fileName)
fileDims <- as.list(c(fileName, sum(colHeights), sum(colWidths)))
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
# The following code seems a duplicate of the code just above it so commenting out. Dec 21, 2018
# for (figchoice in c( "fig4.facetMapRR_IncDelta", "fig3.facetMapRR_2010",
# "figS10.1.facetMapMRV_2010", "figS10.2.facetMapMRV_IncDelta")) {
# plotNameList <- paste(prefix, "_", get(figchoice), sep = "")
# plotNumberList <- which(graphNames %in% plotNameList)
# cat("\facet plotNumberList:", plotNumberList, "\n")
# fileName <- paste(finalDir, figchoice, ".", suffix, ".", fileouttype, sep = "")
# colWidths <- 7
# colHeights <- 6
# g.out <- grid.arrange(
# grobs = graphsListHolder[plotNumberList],
# ncol = 1, nrow = 1,
# layout_matrix = layout,
# widths = colWidths, heights = colHeights
# )
# ggsave(file = fileName, plot = g.out, width = sum(colWidths), height = sum(colHeights) +1, device = fileouttype.device)
# embed_fonts(fileName, outfile=fileName)
# fileDims <- as.list(c(fileName, sum(colHeights), sum(colWidths)))
# pdfDimensions <- rbind(pdfDimensions, fileDims)
# }
#' Fig 1 budget, combines bar charts and box plots; box plots not for tenregions -----
fig1.budgetShare <- paste(c("budgetShare", "budgetShareBoxPlot_2050"), "_", "WB", ".", suffix, sep = "")
for (figchoice in c("fig1.budgetShare")) {
rowNum <- 2
legendNum <- legendHorizontalNum
layout <- layoutMatrix2
colWidths <- colWidths2
colHeights <-heights2
fileName <- paste(finalDir, figchoice, "_", aggChoice = "WB", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
#' Fig S4 availability -----
#' foodgroup availability ratio part 1 - 6 graphs
figS4.foodavail.1 <- paste(c("foodAvail_foodGroup_alcohol", "foodAvail_foodGroup_beverages",
"foodAvail_foodGroup_cereals", "foodAvail_foodGroup_dairy",
"foodAvail_foodGroup_eggs", "foodAvail_foodGroup_fish"), "_", "WB", ".", suffix, sep = "")
#' foodgroup availability part 2 - 6 graphs
figS4.foodavail.2 <- paste(c("foodAvail_foodGroup_fruits", "foodAvail_foodGroup_meats",
"foodAvail_foodGroup_nutsNseeds", "foodAvail_foodGroup_oils",
"foodAvail_foodGroup_pulses", "foodAvail_foodGroup_rootsNPlantain"), "_", "WB", ".", suffix, sep = "")
#' foodgroup availability", part 3 - 2 graphs
figS4.foodavail.3 <- paste(c("foodAvail_foodGroup_sweeteners", "foodAvail_foodGroup_vegetables"), "_", "WB", ".", suffix, sep = "")
#' Fig 2 micronutrients adequacy ratio ------
#' micronutrients adequacy", "part 2 and 3 vitamins
figS7.2.adequacy.vits_1<- paste(c("reqRatio_vits_folate_µg", "reqRatio_vits_niacin_mg",
"reqRatio_vits_riboflavin_mg", "reqRatio_vits_thiamin_mg",
"reqRatio_vits_vit_a_rae_µg", "reqRatio_vits_vit_b6_mg"), "_", "WB", ".", suffix, sep = "")
figS7.2.adequacy.vits_2 <- paste(c("reqRatio_vits_vit_b12_µg", "reqRatio_vits_vit_c_mg",
"reqRatio_vits_vit_d_µg", "reqRatio_vits_vit_e_mg",
"reqRatio_vits_vit_k_µg"), "_", "WB", ".", suffix, sep = "")
# vits candidates for removal - niacin, thiamin, vitamin b6
#' micronutrients adequacy", "part 1 minerals
figS7.3.adequacy.minrls <- paste(c("reqRatio_minrls_calcium_mg", "reqRatio_minrls_iron_mg",
"reqRatio_minrls_magnesium_mg", "reqRatio_minrls_phosphorus_mg",
"reqRatio_minrls_potassium_g", "reqRatio_minrls_zinc_mg"), "_", "WB", ".", suffix, sep = "")
#' Fig S2 kcal availability - 1 graph
figS5.energyavail.WB <- paste(c("kcals.tot.perDay"), "_", "WB", ".", suffix, sep = "")
figS12.budgetShare <- paste(c("budgetShare"), "_", "tenregions", ".", suffix, sep = "")
figS14.energyavail.10regions <- paste(c("kcals.tot.perDay"), "_", "tenregions", ".", suffix, sep = "")
#' Fig s7.0 macro nutrients adequacy ratio, 3 plots per page
figS7.0.adequacy.macro <- paste(c("reqRatio_macro_carbohydrate_g", "reqRatio_macro_protein_g",
"reqRatio_macro_totalfiber_g"), "_", "WB", ".", suffix, sep = "")
#' #' Fig 2 minrl nutrients adequacy ratio, 6 plots per page
#' fig2.adequacy.minrls <- paste(c("minrls_calcium_mg", "minrls_iron_mg", "minrls_magnesium_mg", "minrls_phosphorus_mg",
#' "minrls_potassium_g", "minrls_zinc_mg"), "_", "WB", ".", suffix, sep = "")
#'
#' #' Fig 2 vits 1 nutrients adequacy ratio, 6 plots per page
#' fig2.adequacy.vits.1 <- paste(c("vits_folate_µg", "vits_niacin_mg", "vits_riboflavin_mg", "vits_thiamin_mg",
#' "vits_vit_a_rae_µg", "vits_vit_b6_mg" ), "_", "WB", ".", suffix, sep = "")
#'
#' #' Fig 2 vits 2 nutrients adequacy ratio, 5 plots per page
#' fig2.adequacy.vits. <- paste(c("vits_vit_b6_µg", "vits_vit_c_mg", "vits_vit_d_µg", "vits_vit_e_mg",
#' "vits_vit_k_µg"), "_", "WB", ".", suffix, sep = "")
#' Fig macro AMDRs ------, 3 plots per page
fig2.AMDRhiLo <- paste(c("AMDRShare_carbohydrate_g", "AMDRShare_protein_g",
"AMDRShare_fat_g"), "_", "WB", ".", suffix, sep = "")
figS16.AMDRhiLo <- paste(c("AMDRShare_carbohydrate_g", "AMDRShare_protein_g",
"AMDRShare_fat_g"), "_", "tenregions", ".", suffix, sep = "")
# minrls candidates for removal - magnesium, phosphorus
#' Fig 5 composite DI and nutrient balance ------
figS8.compDINB <- paste(c("compDI", "NutBalScore"), "_", "WB", ".", suffix, sep = "")
figS18.compDINB <- paste(c("compDI", "NutBalScore"), "_", "tenregions", ".", suffix, sep = "")
#' figS8 x Rao and nonstaple share ------
figS8.RaoNenergyShareNonStaples <- paste(c("nonStapleShare", "RAOqe"), "_", "WB", ".", suffix, sep = "")
#' figSS6. Ratio of disqualifying nutrient to its MRV
figS11.badRatios <- paste(c("badRatios_ethanol_g", "badRatios_ft_acds_tot_sat_g", "badRatios_sugar_g"), "_", "WB", ".", suffix, sep = "")
#' Fig S8 availability -----
#' foodgroup availability ratio part 1 - 6 graphs
figS13.foodavail.1 <- paste(c("foodAvail_foodGroup_alcohol", "foodAvail_foodGroup_beverages",
"foodAvail_foodGroup_cereals", "foodAvail_foodGroup_dairy",
"foodAvail_foodGroup_eggs", "foodAvail_foodGroup_fish"), "_", "tenregions", ".", suffix, sep = "")
#' foodgroup availability part 2 - 6 graphs
figS13.foodavail.2 <- paste(c("foodAvail_foodGroup_fruits", "foodAvail_foodGroup_meats",
"foodAvail_foodGroup_nutsNseeds", "foodAvail_foodGroup_oils",
"foodAvail_foodGroup_pulses", "foodAvail_foodGroup_rootsNPlantain"), "_", "tenregions", ".", suffix, sep = "")
#' foodgroup availability", part 3 - 2 graphs
figS13.foodavail.3 <- paste(c("foodAvail_foodGroup_sweeteners", "foodAvail_foodGroup_vegetables"), "_", "tenregions", ".", suffix, sep = "")
#' Fig S17 tenregions micronutrients adequacy ratio ------
#' micronutrients adequacy", "part 2 and 3 vitamins
figS17.1.adequacy.vits <- paste(c("reqRatio_vits_folate_µg", "reqRatio_vits_niacin_mg",
"reqRatio_vits_riboflavin_mg", "reqRatio_vits_thiamin_mg",
"reqRatio_vits_vit_a_rae_µg", "reqRatio_vits_vit_b6_mg"), "_", "tenregions", ".", suffix, sep = "")
figS17.2.adequacy.vits <- paste(c("reqRatio_vits_vit_b12_µg", "reqRatio_vits_vit_c_mg",
"reqRatio_vits_vit_d_µg", "reqRatio_vits_vit_e_mg",
"reqRatio_vits_vit_k_µg"), "_", "tenregions", ".", suffix, sep = "")
# vits candidates for removal - niacin, thiamin, vitamin b6
#' micronutrients adequacy", "part 1 minerals
figS17.3.adequacy.minrls <- paste(c("reqRatio_minrls_calcium_mg", "reqRatio_minrls_iron_mg",
"reqRatio_minrls_magnesium_mg", "reqRatio_minrls_phosphorus_mg",
"reqRatio_minrls_potassium_g", "reqRatio_minrls_zinc_mg"), "_", "tenregions", ".", suffix, sep = "")
figS15.adequacy.macro <- paste(c("reqRatio_macro_carbohydrate_g", "reqRatio_macro_protein_g",
"reqRatio_macro_totalfiber_g"), "_", "tenregions", ".", suffix, sep = "")
#' figS with 6 plots -----
rowNum <- 4
legendNum <- legendHorizontalNum
layout <- layoutMatrix6
colWidths <- colWidths2
colHeights <-heights6
for (figchoice in c( "figS7.2.adequacy.vits_1", "figS7.3.adequacy.minrls" )) {
cat("\nfigchoice:", figchoice, "\n")
fileName <- paste(finalDir, figchoice, "_", "WB", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
for (figchoice in c("figS4.foodavail.1", "figS4.foodavail.2")) {
cat("\nfigchoice:", figchoice, "\n")
fileName <- paste(finalDir, figchoice, "_", "WB", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
for (figchoice in c( "figS13.foodavail.1", "figS13.foodavail.2", "figS17.1.adequacy.vits", "figS17.3.adequacy.minrls")) {
cat("\nfigchoice:", figchoice, "\n")
fileName <- paste(finalDir, figchoice, "_", "tenregions", ".", suffix, ".", fileouttype, sep = "")
cat("fileName: ", fileName, "\n")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
#' figS with 5 plots -----
for (figchoice in c("figS7.2.adequacy.vits_2")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 3
legendNum <- legendVerticalNum
layout <- layoutMatrix5
colWidths <- colWidths2
colHeights <-heights5
fileName <- paste(finalDir, figchoice, "_", "WB", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
for (figchoice in c("figS17.2.adequacy.vits")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 3
legendNum <- legendVerticalNum
layout <- layoutMatrix5
colWidths <- colWidths2
colHeights <-heights5
fileName <- paste(finalDir, figchoice, "_", "tenregions", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
#' figS with 1 plot and horizontal legend at bottom
for (figchoice in c("figS5.energyavail.WB")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 2
legendNum <- legendHorizontalNum
layout <- layoutMatrix1
colWidths <- 5.8
colHeights <- heights1
plotNameList <- paste(prefix, "_", get(figchoice), sep = "")
plotNumberList <- which(graphNames %in% plotNameList)
plotNumberList <- c(plotNumberList, legendNum)
g.out <- grid.arrange(
grobs = graphsListHolder[plotNumberList],
ncol = length(colWidths), nrow = rowNum,
layout_matrix = layout,
widths = colWidths, heights = colHeights
)
fileName <- paste(finalDir, figchoice, ".", suffix, ".", fileouttype, sep = "")
fileDims <- as.list(c(fileName, sum(colHeights), sum(colWidths)))
# ggsave(file = fileName, plot = g.out, width = sum(colWidths), height = sum(colHeights))
ggsave(file = fileName, plot = g.out, width = sum(colWidths), height = sum(colHeights) +1, device = fileouttype.device)
embed_fonts(fileName, outfile=fileName)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
for (figchoice in c("figS12.budgetShare")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 2
legendNum <- legendHorizontalNum
layout <- layoutMatrix1
colWidths <- 5.8
colHeights <- heights1
plotNameList <- paste(prefix, "_", get(figchoice), sep = "")
plotNumberList <- which(graphNames %in% plotNameList)
plotNumberList <- c(plotNumberList, legendNum)
g.out <- grid.arrange(
grobs = graphsListHolder[plotNumberList],
ncol = length(colWidths), nrow = rowNum,
layout_matrix = layout,
widths = colWidths, heights = colHeights
)
fileName <- paste(finalDir, figchoice, "_", aggChoice = "tenregions", ".", suffix, ".", fileouttype, sep = "")
fileDims <- as.list(c(fileName, sum(colHeights), sum(colWidths)))
ggsave(file = fileName, plot = g.out, width = sum(colWidths), height = sum(colHeights), device = fileouttype.device)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
for (figchoice in c("figS14.energyavail.10regions")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 2
legendNum <- legendHorizontalNum
layout <- layoutMatrix1
colWidths <- 5.8
colHeights <- heights1
plotNameList <- paste(prefix, "_", get(figchoice), sep = "")
plotNumberList <- which(graphNames %in% plotNameList)
plotNumberList <- c(plotNumberList, legendNum)
g.out <- grid.arrange(
grobs = graphsListHolder[plotNumberList],
ncol = length(colWidths), nrow = rowNum,
layout_matrix = layout,
widths = colWidths, heights = colHeights
)
fileName <- paste(finalDir, figchoice, "_", aggChoice = "tenregions", ".", suffix, ".", fileouttype, sep = "")
fileDims <- as.list(c(fileName, sum(colHeights), sum(colWidths)))
# ggsave(file = fileName, plot = g.out, width = sum(colWidths), height = sum(colHeights))
ggsave(file = fileName, plot = g.out, width = sum(colWidths), height = sum(colHeights) +1, device = fileouttype.device)
embed_fonts(fileName, outfile=fileName)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
#' figS with 2 plots -----
for (figchoice in c("figS4.foodavail.3", "figS8.compDINB", "figS8.RaoNenergyShareNonStaples")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 2
legendNum <- legendHorizontalNum
layout <- layoutMatrix2
colWidths <- colWidths2
colHeights <-heights2
fileName <- paste(finalDir, figchoice, "_", "WB", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
for (figchoice in c("figS13.foodavail.3", "figS18.compDINB")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 2
legendNum <- legendHorizontalNum
layout <- layoutMatrix2
colWidths <- colWidths2
colHeights <-heights2
fileName <- paste(finalDir, figchoice, "_", "tenregions", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
#' figS with 3 plots -----
for (figchoice in c("fig2.AMDRhiLo", "figS7.0.adequacy.macro", "figS11.badRatios")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 2
legendNum <- legendVerticalNum
layout <- layoutMatrix3
colWidths <- colWidths2
colHeights <-heights3
fileName <- paste(finalDir, figchoice, "_", "WB", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
for (figchoice in c("figS15.adequacy.macro", "figS16.AMDRhiLo")) {
cat("\nfigchoice:", figchoice, "\n")
rowNum <- 2
legendNum <- legendVerticalNum
layout <- layoutMatrix3
colWidths <- colWidths2
colHeights <-heights3
fileName <- paste(finalDir, figchoice, "_", "tenregions", ".", suffix, ".", fileouttype, sep = "")
fileDims <- layoutPlots(fileName, figchoice, prefix, rowNum, legendNum, layout, colHeights = colHeights, colWidths = colWidths)
pdfDimensions <- rbind(pdfDimensions, fileDims)
}
# } commented out switchloop Nov 15.
dt.finalGraphicsNames <- as.data.table(read_csv("data-raw/finalGraphicsNames.csv"), col_names = TRUE)
for (i in 1:nrow(dt.finalGraphicsNames)){
fileFrom <- paste0(fileloc("gDir"), "/final/", dt.finalGraphicsNames$X1[i])
fileTo <- paste0(fileloc("gDir"), "/final/", dt.finalGraphicsNames$X2[i])
file.rename(fileFrom, fileTo)
}
# combine selected pdfs using staple_pdf from package staplr
# fig2list.in <- c("figure2.0.pdf", "figure2.1.pdf", "figure2.2.pdf", "figure2.3.pdf")
# fig2list.out <- "figure2.pdf"
figS4list.in <- c("figureS4.1.pdf", "figureS4.2.pdf", "figureS4.3.pdf")
figS4list.out <- "figureS4.pdf"
figS10list.in <- c("figureS10.1.pdf", "figureS10.2.pdf", "figureS10.3.pdf")
figS10list.out <- "figureS10.pdf"
figS13list.in <- c("figures13.1.pdf", "figures13.2.pdf", "figures13.3.pdf")
figS13list.out <- "figures13.pdf"
figS17list.in <- c("figures17.1.pdf", "figures17.2.pdf", "figures17.3.pdf")
figS17list.out <- "figures17.pdf"
input_directory <- paste0(fileloc("gDir"), "/final")
lists <- c("figS4", "figS9", "figS13", "figS17")
# create one pdf out of several
for (i in 1:length(lists)){
list.in <- get(paste0(lists[i], "list.in"))
list.out <- get(paste0(lists[i], "list.out"))
input_directory <- paste0(fileloc("gDir"), "/final")
output_filepath <- paste(input_directory, list.out, sep = "/")
staple_pdf(input_files = paste(input_directory, list.in, sep = "/"),
output_filepath = output_filepath)
}
createScriptMetaData()
inDT <- pdfDimensions
outName <- "pdfDimensions"
desc <- "final graph file name, height and width"
cleanup(inDT, outName, fileloc("gDir"), desc = desc)
# how to get rid of x axis labels for the first graph in listHolder
# temp <- graphsListHolder[[1]]
# temp + theme(axis.title.x=element_blank(),
# + axis.text.x=element_blank(),
# + axis.ticks.x=element_blank())
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.