R/nbFigur.R
In ybkamaleri/nbReg: Resultattjeneste for Barnediabetesregisteret (BDR)
##' Valgt av sykehus og rapport
##'
##' Her skal deg gjøres valg av sykehus for sammenligne og type rapport
##'
##' @param data Datasettet
##' @param sykehus Utvalgte sykehus
##' @param rapportValg Rapport valg
##' @param yAksen Y aksen for figuren
##' @param save Filnavn for å lage figuren
##' @param format Figur format i.e "pdf", "jpg" eller "png"
##' @param path Hvor skal figuren lagres evt. hjemme område
##'
##' @import dplyr
##' @import ggplot2
##'
##' @export
nbFigur <- function(data = NULL, sykehus = NULL, rapportValg = NULL, yAksen = NULL,
save = NULL, format = "pdf", path = NULL) {
if (is.null(data)) {utData <- nbSelectVar()} else {utData <- data}
## Hente data ut
RegDataValg <- utData$data
xScale <- utData$xScale
figT <- utData$figT
figTxt <- utData$figTxt
xLab <- utData$xLab
xBreaks <- utData$xBreaks
## Ifelse %||%
"%||%" <- function(a,b) if (!is.null(a)) a else b
## Omdefinere variablene
sykehus <- sykehus %||% Sykehus
rapportValg <- rapportValg %||% RapportValg
yAksen <- yAksen %||% YAksen
####################################################
### Data utvalg for å sammenligne sykehus og landet
####################################################
## Valg av sykehuset 1:lokal 2:Resten
samSyk <- lazyeval::interp(~f(var1 %in% sykehus, 1, 2),
.values = list(f = as.name("ifelse"),
var1 = as.name("SykehusKode")))
group <- "SykehusValg"
RegDataValg <- dplyr::mutate_(.data = RegDataValg,
.dots = setNames(list(samSyk), group))
################################################################
### rapportValg 1:Hele, 2:Lokal, 3:Øvrige/Lokal [RegDataValgSam]
################################################################
##-- Hele landet --##
if (rapportValg == 1 & yAksen %in% 1:2) {
RegDataValgSam <- mutate(.data = RegDataValg,
SykehusValg = 1)
## Prosent
RegDataPA <- RegDataValgSam %>%
group_by(Variabel) %>%
tally %>%
mutate(yAksen = (100*n/sum(n)),
samSyk = 1)
##Antall
if (yAksen == 2) {
RegDataPA <- RegDataPA %>%
select(Variabel, samSyk, yAksen=n)
} else { RegDataPA = RegDataPA }
}
## -- Lokal vs andre sykehus --##
RegDataValgSam1 <- filter(RegDataValg, SykehusValg==1) #lokal
RegDataValgSam2 <- filter(RegDataValg, SykehusValg==2) #andre
if (rapportValg %in% 2:3 & yAksen %in% 1:2) {
## Prosent
RegDataPA <- RegDataValgSam1 %>%
group_by(Variabel) %>%
tally %>%
mutate(yAksen = (100*n/sum(n)),
samSyk = 1)
## Antall
if (yAksen == 2) {
RegDataPA <- RegDataPA %>%
select(Variabel, samSyk, yAksen=n)
} else { RegDataPA = RegDataPA }
if (rapportValg == 3) { #andre sykehus
RegDataPA2 <- RegDataValgSam2 %>%
group_by(Variabel) %>%
tally %>%
mutate(yAksen = (100*n/sum(n)),
samSyk = 2)
if (yAksen == 2) {
RegDataPA2 <- RegDataPA2 %>%
select(Variabel, samSyk, yAksen=n)
} else { RegDataPA2 = RegDataPA2 }
}
}
##########################
### Henter N for figur
##########################
if (rapportValg %in% 2:3) {
sykNavn <- RegDataValg$SykehusNavn[RegDataValg$SykehusKode==sykehus][1]
N <- dim(RegDataValgSam1)[1]
andreN <- dim(RegDataValgSam2)[1]
sykehusNavn <- paste0(sykNavn, " (N = ", N, ") ")
sykehusAndre <- paste0("Øvrige sykehus (N = ", andreN, ") ")}
if (rapportValg == 1) {
N <- dim(RegDataValg)[1]
sykehusNavn <- paste0("Hele landet (N = ", N, ") ")
}
##########################################
### Tekst til Figur
##########################################
titBlank <- ""
figTitle <- c(figT, figTxt)
figSubT = paste(figTitle, collapse = "\n")
txtSpace = length(figTxt)
if (yAksen == 1) yLab="Prosent (%)"
if (yAksen == 2) yLab="Antall pasienter"
if (yAksen == 3) {
maalvar = "hba"
RegDataValg <- select(RegDataValg, -diaVarighet)
yLab = "Gjennomsnitt HbA1c (95% CI)"
}
if (yAksen == 4) {
maalvar = "diaVarighet"
RegDataValg <- select(RegDataValg, -hba)
yLab = "Diabetesvarighet (år)"
}
####################
### FIGURER
####################
## ###########################
## ### Felles figur tema
## FigTh <- function(yL, xL, titB, figS, txtS) {
## theme_bw() + ylab(yL) + xlab(xL) +
## ggtitle(bquote(atop(.(titB),atop(.(figS), "")))) +
## expand_limits(x = 0, y = 0) +
## theme(plot.margin = unit(c(txtS,1,1,1), "lines"),
## plot.title = element_text(hjust = 0, size=18),
## axis.title = element_text(face = "bold", size = 12),
## legend.position = 'top',
## legend.text = element_text(size = 12),
## legend.title = element_blank(),
## axis.text = element_text(size = 11),
## axis.line = element_line(size =.3, color = "#333333"),
## panel.grid.major = element_line(color = "#CCCCCC",
## linetype = 2),
## panel.border = element_blank())
## }
####################################
if (xScale == 1) {
if (yAksen==1) RegDataPA$yAksen = round(RegDataPA$yAksen, 1)
if (yAksen==2) RegDataPA$yAksen = as.numeric(format(RegDataPA$yAksen, digits=0))
if (yAksen %in% 1:2 & rapportValg %in% 1:2) {
RegFig <- ggplot(RegDataPA, aes(x=Variabel, y=yAksen, fill=factor(0))) +
geom_bar(stat = "identity") +
scale_x_continuous(breaks = xBreaks) +
scale_fill_manual(name="", values = "#6699CC", label=sykehusNavn) +
geom_text(aes(label=yAksen), vjust=-0.25, colour = "black") +
theme_light() + ylab(yLab) + xlab(xLab) +
ggtitle(bquote(atop(.(titBlank),atop(.(figSubT), "")))) +
expand_limits(x = 0, y = 0) +
theme(plot.margin = unit(c(txtSpace,1,1,1), "lines"),
plot.title = element_text(hjust = 0, size=18),
axis.title = element_text(face = "bold", size = 12),
legend.position = 'top',
legend.text = element_text(size = 12),
legend.title = element_blank(),
axis.text = element_text(size = 11),
axis.line = element_line(size =.3, color = "#333333"),
panel.grid.major = element_line(color = "#CCCCCC",
linetype = 2),
panel.border = element_blank())
}
if (yAksen %in% 1:2 & rapportValg == 3) {
if (yAksen==1) RegDataPA$yAksen = round(RegDataPA$yAksen, 1)
if (yAksen==2) RegDataPA$yAksen = as.numeric(format(RegDataPA$yAksen, digits=0))
if (yAksen==1) {RegDataPA2$yAksen = round(RegDataPA2$yAksen, 1)}
if (yAksen==2) {RegDataPA2$yAksen = as.numeric(format(RegDataPA2$yAksen, digits=0))}
RegFig <- ggplot(NULL, aes(x=Variabel, y=yAksen)) +
geom_bar(data = RegDataPA, aes(fill="syk1",
shape="syk1"), stat = "identity") +
geom_point(data = RegDataPA2, aes(shape= "syk2",
fill= "syk2"),
stat = "identity", size = 5, shape = 23) +
scale_fill_manual(values = c("#6699CC","#000099"),
labels = c("syk1" = sykehusNavn, "syk2" = sykehusAndre)) +
scale_x_continuous(breaks = xBreaks) +
guides(fill = guide_legend(override.aes = list(shape = NA))) +
theme_light() + ylab(yLab) + xlab(xLab) +
ggtitle(bquote(atop(.(titBlank),atop(.(figSubT), "")))) +
expand_limits(x = 0, y = 0) +
theme(plot.margin = unit(c(txtSpace,1,1,1), "lines"),
plot.title = element_text(hjust = 0, size=18),
axis.title = element_text(face = "bold", size = 12),
legend.position = 'top',
legend.text = element_text(size = 12),
legend.title = element_blank(),
axis.text = element_text(size = 11),
axis.line = element_line(size =.3, color = "#333333"),
panel.grid.major = element_line(color = "#CCCCCC",
linetype = 2),
panel.border = element_blank())
}
}
##-------------------------##
##-- Kategorisk variabel --##
##-------------------------##
if (xScale == 2) {
if (yAksen %in% 1:2 & rapportValg %in% 1:2) {
if (yAksen==1) RegDataPA$yAksen=as.numeric(sprintf("%.1f", RegDataPA$yAksen))
if (yAksen==2) RegDataPA$yAksen=as.numeric(sprintf("%.f", RegDataPA$yAksen))
RegFig <- ggplot(RegDataPA, aes(x=Variabel, y=yAksen, fill = factor(samSyk))) +
geom_bar(stat = "identity") +
expand_limits(x = 0, y = 0) +
ylab(yLab) + xlab(xLab) +
scale_fill_manual(name="", values = "#6699CC", label=sykehusNavn) +
geom_text(aes(label=yAksen), vjust=-0.25, colour = "black") +
ggtitle(bquote(atop(.(titBlank),atop(.(figSubT), "")))) +
theme_light() +
theme(plot.margin = unit(c(txtSpace,1,1,1), "lines"),
plot.title = element_text(hjust = 0, size=18),
axis.title = element_text(face = "bold", size = 12),
legend.position = 'top',
legend.text = element_text(size = 12),
legend.title = element_blank(),
axis.text = element_text(size = 11),
axis.line = element_line(size =.3, color = "#333333"),
panel.grid.major = element_line(color = "#CCCCCC",
linetype = 2),
panel.border = element_blank())
}
if (yAksen %in% 1:2 & rapportValg == 3) {
if (yAksen==1) RegDataPA$yAksen=as.numeric(sprintf("%.1f", RegDataPA$yAksen))
if (yAksen==2) RegDataPA$yAksen=as.numeric(sprintf("%.f", RegDataPA$yAksen))
if (yAksen==1) RegDataPA2$yAksen=as.numeric(sprintf("%.1f", RegDataPA2$yAksen))
if (yAksen==2) RegDataPA2$yAksen=as.numeric(sprintf("%.f", RegDataPA2$yAksen))
lengthVar <- if (length(RegDataPA$Variabel) > length(RegDataPA2$Variabel)) {
length(RegDataPA$Variabel) } else { length(RegDataPA2$Variabel)}
RegFig <- ggplot(NULL, aes(x=Variabel, y=yAksen)) +
geom_bar(data = RegDataPA, aes(fill="syk1",
shape="syk1"), stat = "identity") +
geom_point(data = RegDataPA2, aes(shape= "syk2",
fill= "syk2"),
stat = "identity", size = 5, shape = 23) +
ylab(yLab) +
xlab(xLab) +
ggtitle(bquote(atop(.(titBlank),atop(.(figSubT), "")))) +
## scale_shape_manual(values = c(NA, 23),
## labels = c("syk1" = sykehusNavn, "syk2" = sykehusAndre)) +
scale_fill_manual(values = c("#6699CC", "#000099"),
labels = c("syk1" = sykehusNavn, "syk2" = sykehusAndre)) +
guides(fill = guide_legend(override.aes = list(shape = NA))) +
scale_x_discrete(limits = xBreaks[1:max(lengthVar)]) +
theme_light() +
theme(plot.margin = unit(c(txtSpace,1,1,1), "lines"),
plot.title = element_text(hjust = 0, size=18),
axis.title = element_text(face = "bold", size = 12),
legend.position = 'top',
legend.text = element_text(size = 12),
legend.title = element_blank(),
axis.text = element_text(size = 11),
axis.line = element_line(size =.3, color = "#333333"),
panel.grid.major = element_line(color = "#CCCCCC",
linetype = 2),
panel.border = element_blank())
}
}
############################
###Figur for hbalc og ..
############################
##-------------------------##
##-- Kontinuell variabel --##
##-------------------------##
if (xScale == 1) {
## -- Landet og Lokal sykehus --##
if (yAksen %in% 3:4 & rapportValg %in% 1:2) {
if (rapportValg == 2) {
RegDataValg <- filter(.data=RegDataValg, SykehusValg==1)
} else { RegDataValg }
## Antall n eksludert NA for legend
if (rapportValg == 1) {
N <- sum(complete.cases(RegDataValg))
sykehusNavn <- paste0("Hele landet (N = ", N, ") ")
}
if (rapportValg == 2) {
sykNavn <- RegDataValg$SykehusNavn[RegDataValg$SykehusKode==sykehus][1]
lokalRD = filter(.data=RegDataValg, SykehusValg==1)
N = sum(complete.cases(lokalRD))
sykehusNavn <- paste0(sykNavn, " (N = ", N, ") ")
}
RegDataHA <- sumCI(data=RegDataValg, maalvar = maalvar,
gpvars = "Variabel")
## Ta bort Mean når n=1
RegDataHA$Mean[RegDataHA$N<=1] <- 0
## Lage dummy for legend
RegDataHA <- mutate(.data = RegDataHA, samSyk = 1 )
## ## Errorbar for 1 SE
## RegFig <- ggplot(RegDataValg, aes(Variabel, hba)) +
## stat_summary(fun.y = mean, geom = "bar", na.rm = T) +
## stat_summary(fun.data = mean_se, geom = "errorbar", na.rm = T, width=.4) +
RegFig <- ggplot(RegDataHA, aes(x=Variabel, y=Mean)) +
geom_bar(aes(fill=factor(samSyk)), position = position_dodge(), stat = "identity") +
geom_errorbar(aes(ymin=Mean-CI, ymax=Mean+CI), width=.3,
position = position_dodge(.9)) +
ylab(yLab) + xlab(xLab) +
scale_x_continuous(breaks = xBreaks) +
ggtitle(bquote(atop(.(titBlank),atop(.(figSubT), "")))) +
scale_fill_manual(name="", values = "#6699CC", label=sykehusNavn) +
## geom_text(aes(label=yAksen), vjust=-0.25, colour = "black") +
theme_light() +
theme(plot.margin = unit(c(txtSpace,1,1,1), "lines"),
plot.title = element_text(hjust = 0, size=18),
axis.title = element_text(face = "bold", size = 12),
legend.position = 'top',
legend.text = element_text(size = 12),
legend.title = element_blank(),
axis.text = element_text(size = 11),
axis.line = element_line(size =.3, color = "#333333"),
panel.grid.major = element_line(color = "#CCCCCC",
linetype = 2),
panel.border = element_blank())
}
## -- Lokal vs. Andre sykehus --##
if (yAksen %in% 3:4 & rapportValg == 3 ) {
## Antall N lokal og andre
if (rapportValg == 3) {
sykNavn = RegDataValg$SykehusNavn[RegDataValg$SykehusKode==sykehus][1]
lokalRD = filter(.data=RegDataValg, SykehusValg==1)
andreRD = filter(.data=RegDataValg, SykehusValg==2)
N = sum(complete.cases(lokalRD))
andreN = sum(complete.cases(andreRD))
sykehusNavn = paste0(sykNavn, " (N = ", N, ") ")
sykehusAndre = paste0("Øvrige sykehus (N = ", andreN, ") ")
}
RegDataHA <- sumCI(data=RegDataValg, maalvar = maalvar,
gpvars = c("Variabel","SykehusValg"))
## Ta bort Mean når n=1
RegDataHA$Mean[RegDataHA$N<=1] <- 0
## ## Errorbar for 1 SE
## RegFig <- ggplot(RegDataValg, aes(Variabel, hba, fill=factor(SykehusValg))) +
## stat_summary(fun.y = mean, geom = "bar", position = "dodge", na.rm = T) +
## stat_summary(fun.data = mean_se, geom = "errorbar", na.rm = T,
## position = position_dodge(width = 0.9), width=0.4) +
## Errorbar for CI
RegFig <- ggplot(RegDataHA, aes(x=Variabel, y=Mean, fill=factor(SykehusValg))) +
geom_bar(position = position_dodge(), stat = "identity") +
geom_errorbar(aes(ymin=Mean-CI, ymax=Mean+CI), width=.3,
position = position_dodge(.9)) +
ylab(yLab) +
xlab(xLab) +
ggtitle(bquote(atop(.(titBlank),atop(.(figSubT), "")))) +
## scale_shape_manual(values = c(NA, 23),
## labels = c("syk1" = sykehusNavn, "syk2" = sykehusAndre))
scale_fill_manual(values = c("#6699CC","#000099"),
breaks = c("1", "2"),
labels = c(sykehusNavn, sykehusAndre)) +
scale_x_continuous(breaks = xBreaks) +
theme_light() +
theme(plot.margin = unit(c(txtSpace,1,1,1), "lines"),
plot.title = element_text(hjust = 0, size=18),
axis.title = element_text(face = "bold", size = 12),
legend.position = 'top',
legend.text = element_text(size = 12),
legend.title = element_blank(),
axis.text = element_text(size = 11),
axis.line = element_line(size =.3, color = "#333333"),
panel.grid.major = element_line(color = "#CCCCCC",
linetype = 2),
panel.border = element_blank())
}
}
##-------------------------##
##-- Kategorisk variabel --##
##-------------------------##
if (xScale == 2) {
## -- Landet og Lokal sykehus --##
if (yAksen %in% 3:4 & rapportValg %in% 1:2) {
if (rapportValg == 2) {
RegDataValg <- filter(.data=RegDataValg, SykehusValg==1)
} else { RegDataValg }
## Antall n eksludert NA for legend
if (rapportValg == 1) {
N <- sum(complete.cases(RegDataValg))
sykehusNavn <- paste0("Hele landet (N = ", N, ") ")
}
if (rapportValg == 2) {
sykNavn <- RegDataValg$SykehusNavn[RegDataValg$SykehusKode==sykehus][1]
lokalRD = filter(.data=RegDataValg, SykehusValg==1)
N = sum(complete.cases(lokalRD))
sykehusNavn <- paste0(sykNavn, " (N = ", N, ") ")
}
## Aggregerte data for figur
RegDataHA <- sumCI(data=RegDataValg, maalvar = maalvar,
gpvars = "Variabel")
## Teller antall kategorisk for valg i x-skale
lengthVar <- length(RegDataHA$Variabel[RegDataHA$N!=0])
## Ta bort n=1 siden det ikke kan beregne Mean
RegDataHA$Mean[RegDataHA$N<=1] <- 0
## Lage dummy for legend
RegDataHA <- mutate(.data = RegDataHA, samSyk = 1 )
print(RegDataHA)
RegFig <- ggplot(RegDataHA, aes(x=Variabel, y=Mean)) +
geom_bar(aes(fill=factor(samSyk)), position = position_dodge(), stat = "identity") +
geom_errorbar(aes(ymin=Mean-CI, ymax=Mean+CI), width=.3,
position = position_dodge(.9)) +
expand_limits(x = 0, y = 0) +
ylab(yLab) + xlab(xLab) +
scale_fill_manual(name="", values = "#6699CC", label=sykehusNavn) +
scale_x_discrete(limits = xBreaks[1:max(lengthVar)]) +
## geom_text(aes(label=yAksen), vjust=-0.25, colour = "black") +
ggtitle(bquote(atop(.(titBlank),atop(.(figSubT), "")))) +
theme_light() +
theme(plot.margin = unit(c(txtSpace,1,1,1), "lines"),
plot.title = element_text(hjust = 0, size=18),
axis.title = element_text(face = "bold", size = 12),
legend.position = 'top',
legend.text = element_text(size = 12),
legend.title = element_blank(),
axis.text = element_text(size = 11),
axis.line = element_line(size =.3, color = "#333333"),
panel.grid.major = element_line(color = "#CCCCCC",
linetype = 2),
panel.border = element_blank())
}
## -- Lokal vs. Andre sykehus --##
if (yAksen %in% 3:4 & rapportValg == 3 ) {
RegDataHA <- sumCI(data=RegDataValg, maalvar = maalvar,
gpvars = c("Variabel","SykehusValg"))
## Teller antall kategorisk for valg i x-skale
lengthVar <- length(unique(RegDataHA$Variabel[RegDataHA$N!=0]))
## Antall N lokal og andre
if (rapportValg == 3) {
sykNavn = RegDataValg$SykehusNavn[RegDataValg$SykehusKode==sykehus][1]
lokalRD = filter(.data=RegDataValg, SykehusValg==1)
andreRD = filter(.data=RegDataValg, SykehusValg==2)
N = sum(complete.cases(lokalRD))
andreN = sum(complete.cases(andreRD))
sykehusNavn = paste0(sykNavn, " (N = ", N, ") ")
sykehusAndre = paste0("Øvrige sykehus (N = ", andreN, ") ")
}
## Ta bort Mean når n=1
RegDataHA$Mean[RegDataHA$N<=1] <- 0
## Errorbar for CI
RegFig <- ggplot(RegDataHA, aes(x=Variabel, y=Mean, fill=factor(SykehusValg))) +
geom_bar(position = position_dodge(), stat = "identity") +
geom_errorbar(aes(ymin=Mean-CI, ymax=Mean+CI), width=.3,
position = position_dodge(.9)) +
ylab(yLab) +
xlab(xLab) +
ggtitle(bquote(atop(.(titBlank),atop(.(figSubT), "")))) +
scale_fill_manual(values = c("#6699CC", "#000099"),
labels = c(sykehusNavn, sykehusAndre)) +
scale_x_discrete(limits = xBreaks) +
theme_light() +
theme(plot.margin = unit(c(txtSpace,1,1,1), "lines"),
plot.title = element_text(hjust = 0, size=18),
axis.title = element_text(face = "bold", size = 12),
legend.position = 'top',
legend.text = element_text(size = 12),
legend.title = element_blank(),
axis.text = element_text(size = 11),
axis.line = element_line(size =.3, color = "#333333"),
panel.grid.major = element_line(color = "#CCCCCC",
linetype = 2),
panel.border = element_blank())
}
}
###############
### Output
###############
if (is.null(save)) {
print(RegFig)
##ggsave(Save)
##dev.off()
} else {
wdir <- getwd()
path <- path %||% wdir
ggsave(filename = save, device = format)
##print(RegFig)
}
}
ybkamaleri/nbReg documentation built on May 4, 2019, 2:31 p.m.
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##' Valgt av sykehus og rapport
##'
##' Her skal deg gjøres valg av sykehus for sammenligne og type rapport
##'
##' @param data Datasettet
##' @param sykehus Utvalgte sykehus
##' @param rapportValg Rapport valg
##' @param yAksen Y aksen for figuren
##' @param save Filnavn for å lage figuren
##' @param format Figur format i.e "pdf", "jpg" eller "png"
##' @param path Hvor skal figuren lagres evt. hjemme område
##'
##' @import dplyr
##' @import ggplot2
##'
##' @export
nbFigur <- function(data = NULL, sykehus = NULL, rapportValg = NULL, yAksen = NULL,
save = NULL, format = "pdf", path = NULL) {
if (is.null(data)) {utData <- nbSelectVar()} else {utData <- data}
## Hente data ut
RegDataValg <- utData$data
xScale <- utData$xScale
figT <- utData$figT
figTxt <- utData$figTxt
xLab <- utData$xLab
xBreaks <- utData$xBreaks
## Ifelse %||%
"%||%" <- function(a,b) if (!is.null(a)) a else b
## Omdefinere variablene
sykehus <- sykehus %||% Sykehus
rapportValg <- rapportValg %||% RapportValg
yAksen <- yAksen %||% YAksen
####################################################
### Data utvalg for å sammenligne sykehus og landet
####################################################
## Valg av sykehuset 1:lokal 2:Resten
samSyk <- lazyeval::interp(~f(var1 %in% sykehus, 1, 2),
.values = list(f = as.name("ifelse"),
var1 = as.name("SykehusKode")))
group <- "SykehusValg"
RegDataValg <- dplyr::mutate_(.data = RegDataValg,
.dots = setNames(list(samSyk), group))
################################################################
### rapportValg 1:Hele, 2:Lokal, 3:Øvrige/Lokal [RegDataValgSam]
################################################################
##-- Hele landet --##
if (rapportValg == 1 & yAksen %in% 1:2) {
RegDataValgSam <- mutate(.data = RegDataValg,
SykehusValg = 1)
## Prosent
RegDataPA <- RegDataValgSam %>%
group_by(Variabel) %>%
tally %>%
mutate(yAksen = (100*n/sum(n)),
samSyk = 1)
##Antall
if (yAksen == 2) {
RegDataPA <- RegDataPA %>%
select(Variabel, samSyk, yAksen=n)
} else { RegDataPA = RegDataPA }
}
## -- Lokal vs andre sykehus --##
RegDataValgSam1 <- filter(RegDataValg, SykehusValg==1) #lokal
RegDataValgSam2 <- filter(RegDataValg, SykehusValg==2) #andre
if (rapportValg %in% 2:3 & yAksen %in% 1:2) {
## Prosent
RegDataPA <- RegDataValgSam1 %>%
group_by(Variabel) %>%
tally %>%
mutate(yAksen = (100*n/sum(n)),
samSyk = 1)
## Antall
if (yAksen == 2) {
RegDataPA <- RegDataPA %>%
select(Variabel, samSyk, yAksen=n)
} else { RegDataPA = RegDataPA }
if (rapportValg == 3) { #andre sykehus
RegDataPA2 <- RegDataValgSam2 %>%
group_by(Variabel) %>%
tally %>%
mutate(yAksen = (100*n/sum(n)),
samSyk = 2)
if (yAksen == 2) {
RegDataPA2 <- RegDataPA2 %>%
select(Variabel, samSyk, yAksen=n)
} else { RegDataPA2 = RegDataPA2 }
}
}
##########################
### Henter N for figur
##########################
if (rapportValg %in% 2:3) {
sykNavn <- RegDataValg$SykehusNavn[RegDataValg$SykehusKode==sykehus][1]
N <- dim(RegDataValgSam1)[1]
andreN <- dim(RegDataValgSam2)[1]
sykehusNavn <- paste0(sykNavn, " (N = ", N, ") ")
sykehusAndre <- paste0("Øvrige sykehus (N = ", andreN, ") ")}
if (rapportValg == 1) {
N <- dim(RegDataValg)[1]
sykehusNavn <- paste0("Hele landet (N = ", N, ") ")
}
##########################################
### Tekst til Figur
##########################################
titBlank <- ""
figTitle <- c(figT, figTxt)
figSubT = paste(figTitle, collapse = "\n")
txtSpace = length(figTxt)
if (yAksen == 1) yLab="Prosent (%)"
if (yAksen == 2) yLab="Antall pasienter"
if (yAksen == 3) {
maalvar = "hba"
RegDataValg <- select(RegDataValg, -diaVarighet)
yLab = "Gjennomsnitt HbA1c (95% CI)"
}
if (yAksen == 4) {
maalvar = "diaVarighet"
RegDataValg <- select(RegDataValg, -hba)
yLab = "Diabetesvarighet (år)"
}
####################
### FIGURER
####################
## ###########################
## ### Felles figur tema
## FigTh <- function(yL, xL, titB, figS, txtS) {
## theme_bw() + ylab(yL) + xlab(xL) +
## ggtitle(bquote(atop(.(titB),atop(.(figS), "")))) +
## expand_limits(x = 0, y = 0) +
## theme(plot.margin = unit(c(txtS,1,1,1), "lines"),
## plot.title = element_text(hjust = 0, size=18),
## axis.title = element_text(face = "bold", size = 12),
## legend.position = 'top',
## legend.text = element_text(size = 12),
## legend.title = element_blank(),
## axis.text = element_text(size = 11),
## axis.line = element_line(size =.3, color = "#333333"),
## panel.grid.major = element_line(color = "#CCCCCC",
## linetype = 2),
## panel.border = element_blank())
## }
####################################
if (xScale == 1) {
if (yAksen==1) RegDataPA$yAksen = round(RegDataPA$yAksen, 1)
if (yAksen==2) RegDataPA$yAksen = as.numeric(format(RegDataPA$yAksen, digits=0))
if (yAksen %in% 1:2 & rapportValg %in% 1:2) {
RegFig <- ggplot(RegDataPA, aes(x=Variabel, y=yAksen, fill=factor(0))) +
geom_bar(stat = "identity") +
scale_x_continuous(breaks = xBreaks) +
scale_fill_manual(name="", values = "#6699CC", label=sykehusNavn) +
geom_text(aes(label=yAksen), vjust=-0.25, colour = "black") +
theme_light() + ylab(yLab) + xlab(xLab) +
ggtitle(bquote(atop(.(titBlank),atop(.(figSubT), "")))) +
expand_limits(x = 0, y = 0) +
theme(plot.margin = unit(c(txtSpace,1,1,1), "lines"),
plot.title = element_text(hjust = 0, size=18),
axis.title = element_text(face = "bold", size = 12),
legend.position = 'top',
legend.text = element_text(size = 12),
legend.title = element_blank(),
axis.text = element_text(size = 11),
axis.line = element_line(size =.3, color = "#333333"),
panel.grid.major = element_line(color = "#CCCCCC",
linetype = 2),
panel.border = element_blank())
}
if (yAksen %in% 1:2 & rapportValg == 3) {
if (yAksen==1) RegDataPA$yAksen = round(RegDataPA$yAksen, 1)
if (yAksen==2) RegDataPA$yAksen = as.numeric(format(RegDataPA$yAksen, digits=0))
if (yAksen==1) {RegDataPA2$yAksen = round(RegDataPA2$yAksen, 1)}
if (yAksen==2) {RegDataPA2$yAksen = as.numeric(format(RegDataPA2$yAksen, digits=0))}
RegFig <- ggplot(NULL, aes(x=Variabel, y=yAksen)) +
geom_bar(data = RegDataPA, aes(fill="syk1",
shape="syk1"), stat = "identity") +
geom_point(data = RegDataPA2, aes(shape= "syk2",
fill= "syk2"),
stat = "identity", size = 5, shape = 23) +
scale_fill_manual(values = c("#6699CC","#000099"),
labels = c("syk1" = sykehusNavn, "syk2" = sykehusAndre)) +
scale_x_continuous(breaks = xBreaks) +
guides(fill = guide_legend(override.aes = list(shape = NA))) +
theme_light() + ylab(yLab) + xlab(xLab) +
ggtitle(bquote(atop(.(titBlank),atop(.(figSubT), "")))) +
expand_limits(x = 0, y = 0) +
theme(plot.margin = unit(c(txtSpace,1,1,1), "lines"),
plot.title = element_text(hjust = 0, size=18),
axis.title = element_text(face = "bold", size = 12),
legend.position = 'top',
legend.text = element_text(size = 12),
legend.title = element_blank(),
axis.text = element_text(size = 11),
axis.line = element_line(size =.3, color = "#333333"),
panel.grid.major = element_line(color = "#CCCCCC",
linetype = 2),
panel.border = element_blank())
}
}
##-------------------------##
##-- Kategorisk variabel --##
##-------------------------##
if (xScale == 2) {
if (yAksen %in% 1:2 & rapportValg %in% 1:2) {
if (yAksen==1) RegDataPA$yAksen=as.numeric(sprintf("%.1f", RegDataPA$yAksen))
if (yAksen==2) RegDataPA$yAksen=as.numeric(sprintf("%.f", RegDataPA$yAksen))
RegFig <- ggplot(RegDataPA, aes(x=Variabel, y=yAksen, fill = factor(samSyk))) +
geom_bar(stat = "identity") +
expand_limits(x = 0, y = 0) +
ylab(yLab) + xlab(xLab) +
scale_fill_manual(name="", values = "#6699CC", label=sykehusNavn) +
geom_text(aes(label=yAksen), vjust=-0.25, colour = "black") +
ggtitle(bquote(atop(.(titBlank),atop(.(figSubT), "")))) +
theme_light() +
theme(plot.margin = unit(c(txtSpace,1,1,1), "lines"),
plot.title = element_text(hjust = 0, size=18),
axis.title = element_text(face = "bold", size = 12),
legend.position = 'top',
legend.text = element_text(size = 12),
legend.title = element_blank(),
axis.text = element_text(size = 11),
axis.line = element_line(size =.3, color = "#333333"),
panel.grid.major = element_line(color = "#CCCCCC",
linetype = 2),
panel.border = element_blank())
}
if (yAksen %in% 1:2 & rapportValg == 3) {
if (yAksen==1) RegDataPA$yAksen=as.numeric(sprintf("%.1f", RegDataPA$yAksen))
if (yAksen==2) RegDataPA$yAksen=as.numeric(sprintf("%.f", RegDataPA$yAksen))
if (yAksen==1) RegDataPA2$yAksen=as.numeric(sprintf("%.1f", RegDataPA2$yAksen))
if (yAksen==2) RegDataPA2$yAksen=as.numeric(sprintf("%.f", RegDataPA2$yAksen))
lengthVar <- if (length(RegDataPA$Variabel) > length(RegDataPA2$Variabel)) {
length(RegDataPA$Variabel) } else { length(RegDataPA2$Variabel)}
RegFig <- ggplot(NULL, aes(x=Variabel, y=yAksen)) +
geom_bar(data = RegDataPA, aes(fill="syk1",
shape="syk1"), stat = "identity") +
geom_point(data = RegDataPA2, aes(shape= "syk2",
fill= "syk2"),
stat = "identity", size = 5, shape = 23) +
ylab(yLab) +
xlab(xLab) +
ggtitle(bquote(atop(.(titBlank),atop(.(figSubT), "")))) +
## scale_shape_manual(values = c(NA, 23),
## labels = c("syk1" = sykehusNavn, "syk2" = sykehusAndre)) +
scale_fill_manual(values = c("#6699CC", "#000099"),
labels = c("syk1" = sykehusNavn, "syk2" = sykehusAndre)) +
guides(fill = guide_legend(override.aes = list(shape = NA))) +
scale_x_discrete(limits = xBreaks[1:max(lengthVar)]) +
theme_light() +
theme(plot.margin = unit(c(txtSpace,1,1,1), "lines"),
plot.title = element_text(hjust = 0, size=18),
axis.title = element_text(face = "bold", size = 12),
legend.position = 'top',
legend.text = element_text(size = 12),
legend.title = element_blank(),
axis.text = element_text(size = 11),
axis.line = element_line(size =.3, color = "#333333"),
panel.grid.major = element_line(color = "#CCCCCC",
linetype = 2),
panel.border = element_blank())
}
}
############################
###Figur for hbalc og ..
############################
##-------------------------##
##-- Kontinuell variabel --##
##-------------------------##
if (xScale == 1) {
## -- Landet og Lokal sykehus --##
if (yAksen %in% 3:4 & rapportValg %in% 1:2) {
if (rapportValg == 2) {
RegDataValg <- filter(.data=RegDataValg, SykehusValg==1)
} else { RegDataValg }
## Antall n eksludert NA for legend
if (rapportValg == 1) {
N <- sum(complete.cases(RegDataValg))
sykehusNavn <- paste0("Hele landet (N = ", N, ") ")
}
if (rapportValg == 2) {
sykNavn <- RegDataValg$SykehusNavn[RegDataValg$SykehusKode==sykehus][1]
lokalRD = filter(.data=RegDataValg, SykehusValg==1)
N = sum(complete.cases(lokalRD))
sykehusNavn <- paste0(sykNavn, " (N = ", N, ") ")
}
RegDataHA <- sumCI(data=RegDataValg, maalvar = maalvar,
gpvars = "Variabel")
## Ta bort Mean når n=1
RegDataHA$Mean[RegDataHA$N<=1] <- 0
## Lage dummy for legend
RegDataHA <- mutate(.data = RegDataHA, samSyk = 1 )
## ## Errorbar for 1 SE
## RegFig <- ggplot(RegDataValg, aes(Variabel, hba)) +
## stat_summary(fun.y = mean, geom = "bar", na.rm = T) +
## stat_summary(fun.data = mean_se, geom = "errorbar", na.rm = T, width=.4) +
RegFig <- ggplot(RegDataHA, aes(x=Variabel, y=Mean)) +
geom_bar(aes(fill=factor(samSyk)), position = position_dodge(), stat = "identity") +
geom_errorbar(aes(ymin=Mean-CI, ymax=Mean+CI), width=.3,
position = position_dodge(.9)) +
ylab(yLab) + xlab(xLab) +
scale_x_continuous(breaks = xBreaks) +
ggtitle(bquote(atop(.(titBlank),atop(.(figSubT), "")))) +
scale_fill_manual(name="", values = "#6699CC", label=sykehusNavn) +
## geom_text(aes(label=yAksen), vjust=-0.25, colour = "black") +
theme_light() +
theme(plot.margin = unit(c(txtSpace,1,1,1), "lines"),
plot.title = element_text(hjust = 0, size=18),
axis.title = element_text(face = "bold", size = 12),
legend.position = 'top',
legend.text = element_text(size = 12),
legend.title = element_blank(),
axis.text = element_text(size = 11),
axis.line = element_line(size =.3, color = "#333333"),
panel.grid.major = element_line(color = "#CCCCCC",
linetype = 2),
panel.border = element_blank())
}
## -- Lokal vs. Andre sykehus --##
if (yAksen %in% 3:4 & rapportValg == 3 ) {
## Antall N lokal og andre
if (rapportValg == 3) {
sykNavn = RegDataValg$SykehusNavn[RegDataValg$SykehusKode==sykehus][1]
lokalRD = filter(.data=RegDataValg, SykehusValg==1)
andreRD = filter(.data=RegDataValg, SykehusValg==2)
N = sum(complete.cases(lokalRD))
andreN = sum(complete.cases(andreRD))
sykehusNavn = paste0(sykNavn, " (N = ", N, ") ")
sykehusAndre = paste0("Øvrige sykehus (N = ", andreN, ") ")
}
RegDataHA <- sumCI(data=RegDataValg, maalvar = maalvar,
gpvars = c("Variabel","SykehusValg"))
## Ta bort Mean når n=1
RegDataHA$Mean[RegDataHA$N<=1] <- 0
## ## Errorbar for 1 SE
## RegFig <- ggplot(RegDataValg, aes(Variabel, hba, fill=factor(SykehusValg))) +
## stat_summary(fun.y = mean, geom = "bar", position = "dodge", na.rm = T) +
## stat_summary(fun.data = mean_se, geom = "errorbar", na.rm = T,
## position = position_dodge(width = 0.9), width=0.4) +
## Errorbar for CI
RegFig <- ggplot(RegDataHA, aes(x=Variabel, y=Mean, fill=factor(SykehusValg))) +
geom_bar(position = position_dodge(), stat = "identity") +
geom_errorbar(aes(ymin=Mean-CI, ymax=Mean+CI), width=.3,
position = position_dodge(.9)) +
ylab(yLab) +
xlab(xLab) +
ggtitle(bquote(atop(.(titBlank),atop(.(figSubT), "")))) +
## scale_shape_manual(values = c(NA, 23),
## labels = c("syk1" = sykehusNavn, "syk2" = sykehusAndre))
scale_fill_manual(values = c("#6699CC","#000099"),
breaks = c("1", "2"),
labels = c(sykehusNavn, sykehusAndre)) +
scale_x_continuous(breaks = xBreaks) +
theme_light() +
theme(plot.margin = unit(c(txtSpace,1,1,1), "lines"),
plot.title = element_text(hjust = 0, size=18),
axis.title = element_text(face = "bold", size = 12),
legend.position = 'top',
legend.text = element_text(size = 12),
legend.title = element_blank(),
axis.text = element_text(size = 11),
axis.line = element_line(size =.3, color = "#333333"),
panel.grid.major = element_line(color = "#CCCCCC",
linetype = 2),
panel.border = element_blank())
}
}
##-------------------------##
##-- Kategorisk variabel --##
##-------------------------##
if (xScale == 2) {
## -- Landet og Lokal sykehus --##
if (yAksen %in% 3:4 & rapportValg %in% 1:2) {
if (rapportValg == 2) {
RegDataValg <- filter(.data=RegDataValg, SykehusValg==1)
} else { RegDataValg }
## Antall n eksludert NA for legend
if (rapportValg == 1) {
N <- sum(complete.cases(RegDataValg))
sykehusNavn <- paste0("Hele landet (N = ", N, ") ")
}
if (rapportValg == 2) {
sykNavn <- RegDataValg$SykehusNavn[RegDataValg$SykehusKode==sykehus][1]
lokalRD = filter(.data=RegDataValg, SykehusValg==1)
N = sum(complete.cases(lokalRD))
sykehusNavn <- paste0(sykNavn, " (N = ", N, ") ")
}
## Aggregerte data for figur
RegDataHA <- sumCI(data=RegDataValg, maalvar = maalvar,
gpvars = "Variabel")
## Teller antall kategorisk for valg i x-skale
lengthVar <- length(RegDataHA$Variabel[RegDataHA$N!=0])
## Ta bort n=1 siden det ikke kan beregne Mean
RegDataHA$Mean[RegDataHA$N<=1] <- 0
## Lage dummy for legend
RegDataHA <- mutate(.data = RegDataHA, samSyk = 1 )
print(RegDataHA)
RegFig <- ggplot(RegDataHA, aes(x=Variabel, y=Mean)) +
geom_bar(aes(fill=factor(samSyk)), position = position_dodge(), stat = "identity") +
geom_errorbar(aes(ymin=Mean-CI, ymax=Mean+CI), width=.3,
position = position_dodge(.9)) +
expand_limits(x = 0, y = 0) +
ylab(yLab) + xlab(xLab) +
scale_fill_manual(name="", values = "#6699CC", label=sykehusNavn) +
scale_x_discrete(limits = xBreaks[1:max(lengthVar)]) +
## geom_text(aes(label=yAksen), vjust=-0.25, colour = "black") +
ggtitle(bquote(atop(.(titBlank),atop(.(figSubT), "")))) +
theme_light() +
theme(plot.margin = unit(c(txtSpace,1,1,1), "lines"),
plot.title = element_text(hjust = 0, size=18),
axis.title = element_text(face = "bold", size = 12),
legend.position = 'top',
legend.text = element_text(size = 12),
legend.title = element_blank(),
axis.text = element_text(size = 11),
axis.line = element_line(size =.3, color = "#333333"),
panel.grid.major = element_line(color = "#CCCCCC",
linetype = 2),
panel.border = element_blank())
}
## -- Lokal vs. Andre sykehus --##
if (yAksen %in% 3:4 & rapportValg == 3 ) {
RegDataHA <- sumCI(data=RegDataValg, maalvar = maalvar,
gpvars = c("Variabel","SykehusValg"))
## Teller antall kategorisk for valg i x-skale
lengthVar <- length(unique(RegDataHA$Variabel[RegDataHA$N!=0]))
## Antall N lokal og andre
if (rapportValg == 3) {
sykNavn = RegDataValg$SykehusNavn[RegDataValg$SykehusKode==sykehus][1]
lokalRD = filter(.data=RegDataValg, SykehusValg==1)
andreRD = filter(.data=RegDataValg, SykehusValg==2)
N = sum(complete.cases(lokalRD))
andreN = sum(complete.cases(andreRD))
sykehusNavn = paste0(sykNavn, " (N = ", N, ") ")
sykehusAndre = paste0("Øvrige sykehus (N = ", andreN, ") ")
}
## Ta bort Mean når n=1
RegDataHA$Mean[RegDataHA$N<=1] <- 0
## Errorbar for CI
RegFig <- ggplot(RegDataHA, aes(x=Variabel, y=Mean, fill=factor(SykehusValg))) +
geom_bar(position = position_dodge(), stat = "identity") +
geom_errorbar(aes(ymin=Mean-CI, ymax=Mean+CI), width=.3,
position = position_dodge(.9)) +
ylab(yLab) +
xlab(xLab) +
ggtitle(bquote(atop(.(titBlank),atop(.(figSubT), "")))) +
scale_fill_manual(values = c("#6699CC", "#000099"),
labels = c(sykehusNavn, sykehusAndre)) +
scale_x_discrete(limits = xBreaks) +
theme_light() +
theme(plot.margin = unit(c(txtSpace,1,1,1), "lines"),
plot.title = element_text(hjust = 0, size=18),
axis.title = element_text(face = "bold", size = 12),
legend.position = 'top',
legend.text = element_text(size = 12),
legend.title = element_blank(),
axis.text = element_text(size = 11),
axis.line = element_line(size =.3, color = "#333333"),
panel.grid.major = element_line(color = "#CCCCCC",
linetype = 2),
panel.border = element_blank())
}
}
###############
### Output
###############
if (is.null(save)) {
print(RegFig)
##ggsave(Save)
##dev.off()
} else {
wdir <- getwd()
path <- path %||% wdir
ggsave(filename = save, device = format)
##print(RegFig)
}
}
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