demo/haiti/functions_Post_Processing_figures.R
In SwissTPH/CHWplacement: What the Package Does (One Line, Title Case)
#################################
# plotting function from Emilie Pothin
PlotMap=function(img,NAMEfile="",shpFile,colormapDT,Title.legend="", myalpha=1, width_polygon=0.2){
shapefile_df <- fortify(shpFile)
r=as.data.frame(rasterToPoints(img))
names(r)[3]="z"
r$name=NAMEfile
r$z=cut(r$z,unique(c(0,as.numeric(as.character(colormapDT$value)))))
gg<-ggplot(r)+geom_tile(aes(x=x,y=y,fill=factor(as.numeric(z),levels=1:nrow(colormapDT))), alpha=myalpha)+
geom_path(data = shapefile_df,
aes(x = long, y = lat, group = group),
color = 'black',size=width_polygon)+
theme_void()+
coord_fixed()+
theme(panel.border = element_blank())+
scale_fill_manual(Title.legend,breaks=1:nrow(colormapDT),labels=as.character(colormapDT$label), values = as.character(colormapDT$color),drop = FALSE)
return(gg)
}
#################################
# formating scenario files
plot_scenario_all_cslscp=function(CHW.positions, name_scenario){
my.CHW.positions=CHW.positions
my.CHW.positions$count=1
duplicatedCHW=aggregate((my.CHW.positions$count),
by= list(posx=my.CHW.positions$x,posy=my.CHW.positions$y), FUN=(sum))
names(duplicatedCHW)=c("x","y","count")
my.CHW.positions$count=NULL
my.CHW.positions=merge(my.CHW.positions,duplicatedCHW, all.x=TRUE )
my.CHW.positions$capacities=my.CHW.positions$my.list.capa.here/my.CHW.positions$count
my.CHW.positions$scenario=name_scenario
return(my.CHW.positions)
}
plot_scenario_all_cslscp_new_names=function(CHW.positions, name_scenario){
my.CHW.positions=CHW.positions
my.CHW.positions$count=1
duplicatedCHW=aggregate((my.CHW.positions$count),
by= list(posx=my.CHW.positions$x,posy=my.CHW.positions$y), FUN=(sum))
names(duplicatedCHW)=c("x","y","count")
my.CHW.positions$count=NULL
my.CHW.positions=merge(my.CHW.positions,duplicatedCHW, all.x=TRUE )
my.CHW.positions$capacities=my.CHW.positions$capacity/my.CHW.positions$count
my.CHW.positions$scenario=name_scenario
return(my.CHW.positions)
}
#################################
# Plot summary file per department
plot_dpt_summary=function(mydpt){
list_dpt3=seccom.shp@data %>% select(NAME_1, ID_1, departement) %>%
unique %>%
mutate(ADM1NAME =gsub("grande", "grand",tolower(gsub(" ", "-", NAME_1))),
dpt =gsub(" ", "", NAME_1),
departement=gsub("Reste", "",gsub(" ", "",
ifelse(departement=="Aire metropolitaine", "AireMetro", departement))))
mydpt_id1=unique(list_dpt3$ID_1[list_dpt3$dpt == mydpt])
mydpt_ADM1NAME=unique(list_dpt3$ADM1NAME[list_dpt3$dpt %in% mydpt])
mydepart=unique(list_dpt3$departement[list_dpt3$dpt %in% mydpt])
my.shp.dpt=subset(seccom.shp, ID_1 == mydpt_id1)
population.dpt=mask(crop(population.haiti, my.shp.dpt), my.shp.dpt)
friction.dpt=mask(crop(friction, my.shp.dpt), my.shp.dpt)
urb.dpt=mask(crop(population.urb.hai.dummy, my.shp.dpt), my.shp.dpt)
access.dpt=mask(crop(access.raster.spa.CCS, my.shp.dpt), my.shp.dpt)
CHW.positions.scenario.dpt.scenarioA=CHW.positions.scenarioA.CSLCP %>% filter(dpt %in% mydepart)
CHW.positions.scenario.dpt.scenarioB=CHW.positions.scenarioB.CSLCP %>% filter(dpt %in% mydepart)
CHW.positions.scenario.dpt.scenarioC=CHW.positions.scenarioC.CSLCP %>% filter(dpt %in% mydepart)
CHW.positions.scenario.dpt.scenarioC2=CHW.positions.scenarioC2.CSLCP %>% filter(dpt %in% mydepart)
CCS.shp.dpt=subset(CCS.shp,ADM1NAME == mydpt_ADM1NAME & SOURCE !="MIS")
CCS.shp.dpt=spTransform(CCS.shp.dpt,newproj)
CCS.dpt=data.frame(CCS.shp.dpt@coords)
map.population.dpt<-PlotMap(population.dpt,Title.legend="Population \ndensity",shpFile=my.shp.dpt,colormapDT=colormapDT0)+theme(legend.key.size = unit(0.16, "in"))
#map.population.dpt
map.friction.dpt<-PlotMap(friction.dpt*1000,Title.legend="Minutes to \ncross 1km ",shpFile=my.shp.dpt,colormapDT=colormapDTb2)+theme(legend.key.size = unit(0.16, "in"))
map.friction.dpt
map.population.dpt_frame=plot_grid(map.population.dpt,labels = c("2.")) +theme(plot.background = element_rect(color = "black"))
#plot_pop_fric
map.friction.dpt_frame=plot_grid(map.friction.dpt,labels = c("3.")) +theme(plot.background = element_rect(color = "black"))
plot_pop_fric=plot_grid(map.population.dpt_frame,
map.friction.dpt_frame,labels = c("2.", "3."), ncol=2)
travel.time.dpt<-PlotMap(access.dpt,Title.legend="Walking time\nto CCS\n(minutes)\n ",shpFile=my.shp.dpt,colormapDT=colormapDTb, myalpha = 0.7)+
geom_point(data=CCS.dpt,aes(x=coords.x1,y=coords.x2, shape="CCS"),col="red")+scale_shape_manual(values=17, name="")
map.A=travel.time.dpt+
geom_point(data=CHW.positions.scenario.dpt.scenarioA,aes(x=x,y=y, group=seq_along(rank), size=count),shape=20,col="dodgerblue")+
labs(size="Number\nof CHWs")
map.B=travel.time.dpt+
geom_point(data=CHW.positions.scenario.dpt.scenarioB,aes(x=x,y=y, group=seq_along(rank), size=count),shape=20,col="dodgerblue")+
labs(size="Number\nof CHWs")
map.C=travel.time.dpt+
geom_point(data=CHW.positions.scenario.dpt.scenarioC,aes(x=x,y=y, group=seq_along(rank), size=count),shape=20,col="dodgerblue")+
labs(size="Number\nof CHWs")
map.C2=travel.time.dpt+
geom_point(data=CHW.positions.scenario.dpt.scenarioC2,aes(x=x,y=y, group=seq_along(rank), size=count),shape=20,col="dodgerblue")+
labs(size="Number\nof CHWs")
legend <- get_legend(map.A + theme(legend.box.margin = margin(0, 0, 0, 0), legend.position = "bottom")+
guides(size=guide_legend(order=2), fill=guide_legend(order=1)))
title <- ggdraw() + draw_label( " 1.", fontface = 'bold', x = 0, hjust = 0 ) + theme(plot.margin = margin(0, 0, 0, 0))
plot_scenarios=plot_grid(map.A+theme(legend.position = "none"),
map.B+theme(legend.position = "none"),
map.C+theme(legend.position = "none"),
map.C2+theme(legend.position = "none") ,
ncol=2, labels = c("A", "B", "C", "C2"))
plot_scenarios_title=plot_grid(title, plot_scenarios, ncol=1,rel_heights = c(0.05,1))
plot_scenarios_legend=plot_grid(plot_scenarios_title, legend, rel_heights = c(1, .1), ncol=1) +
theme(plot.background = element_rect(color = "black"))
#plot_scenarios_legend
all.dpt=plot_grid(plot_scenarios_legend,plot_pop_fric , ncol=1, scale=1,rel_heights = c(2.7,1))
#all.dpt
return(all.dpt)
}
#################################
# Plot gap per section communale
PlotGapScenarioSeccom=function(CHW.positions){
scenario.sp=SpatialPointsDataFrame(CHW.positions,
CHW.positions, #the R object to convert
proj4string = crs(newproj))
scenario.sp <- over(scenario.sp, seccom.shp)
CHW.per.seccom=data.frame(table(scenario.sp$ID_4)) ;names(CHW.per.seccom)=c("ID_4","nbCHW")
CHW.per.seccom=sp::merge(seccom.shp,CHW.per.seccom)
CHW.per.seccom=merge(CHW.per.seccom,spa.seccom,all=TRUE)
CHW.per.seccom@data$nbCHW[is.na(CHW.per.seccom@data$nbCHW)]=0
CHW.per.seccom@data$nbCHWSPA[is.na(CHW.per.seccom@data$nbCHWSPA)]=0
CHW.per.seccom@data$diffSPA=CHW.per.seccom@data$nbCHWSPA-CHW.per.seccom@data$nbCHW
CHW.per.seccom.df <- tidy(CHW.per.seccom)
CHW.per.seccom$polyID <- sapply(slot(CHW.per.seccom, "polygons"), function(x) slot(x, "ID"))
CHW.per.seccom.df <- merge(CHW.per.seccom.df, CHW.per.seccom, by.x = "id", by.y="polyID")
CHW.per.seccom.df$diffSPA.cut=cut(CHW.per.seccom.df$diffSPA, breaks=c(-350,-50,-10,0,10,50,300),
label=c("< -50","-50 to -10","-10 to 0","0 to 10","10 to 50", ">50"),include.lowest=TRUE, right=FALSE)
plot.seccom=ggplot() + # initialize ggplot object
geom_polygon( # make a polygon
data = CHW.per.seccom.df, # data frame
aes(x = long, y = lat, group = group, # coordinates, and group them by polygons
fill = diffSPA.cut)) + # variable to use for filling
#scale_fill_gradient2( name="difference",low="red", high="lightblue",mid="white") +
scale_fill_brewer( name="Difference\nin nb. of CHWs", type="seq", palette="RdBu", drop=FALSE)+
geom_path(data = seccom.shp.union,
aes(x = long, y = lat, group = group),
color = 'black',size=0.2)+
theme(line = element_blank(), # remove axis lines ..
axis.text=element_blank(), # .. tickmarks..
axis.title=element_blank(), # .. axis labels..
panel.background = element_blank(),
legend.key.size = unit(0.5, "cm"),
legend.position = c(0.2, 0.7),
legend.text=element_text(size=8),legend.title=element_text(size=10))+ # .. background gridlines
coord_equal()
return(list("plot"=plot.seccom, "file"=CHW.per.seccom@data))
}
#################################
# Plot total per section communale
PlotScenarioSeccom=function(CHW.positions){
scenario.sp=SpatialPointsDataFrame(CHW.positions[c("x","y")],
CHW.positions, #the R object to convert
proj4string = crs(newproj))
scenario.sp <- over(scenario.sp, seccom.shp)
CHW.per.seccom=data.frame(table(scenario.sp$ID_4)) ;names(CHW.per.seccom)=c("ID_4","nbCHW")
CHW.per.seccom=sp::merge(seccom.shp,CHW.per.seccom)
CHW.per.seccom.df <- tidy(CHW.per.seccom)
CHW.per.seccom$polyID <- sapply(slot(CHW.per.seccom, "polygons"), function(x) slot(x, "ID"))
CHW.per.seccom.df <- merge(CHW.per.seccom.df, CHW.per.seccom, by.x = "id", by.y="polyID")
CHW.per.seccom.df$nbCHW[is.na(CHW.per.seccom.df$nbCHW)]=0
CHW.per.seccom.df$nbCHW.cut=cut(CHW.per.seccom.df$nbCHW, breaks=c(0,10,20,30,40,50,500),
label=c("<10","10 to 20","20 to 30","30 to 40","40 to 50", ">50"), include.lowest=TRUE, right=TRUE)
print(max(CHW.per.seccom.df$nbCHW))
plot.seccom=ggplot() + # initialize ggplot object
geom_polygon( # make a polygon
data = CHW.per.seccom.df, # data frame
aes(x = long, y = lat, group = group, # coordinates, and group them by polygons
fill = nbCHW.cut)) + # variable to use for filling
scale_fill_brewer( name="Nb. of CHWs", type="seq", palette="Reds", drop=FALSE)+
geom_path(data = seccom.shp.union,
aes(x = long, y = lat, group = group),
color = 'black',size=0.2)+
theme(line = element_blank(), # remove axis lines ..
axis.text=element_blank(), # .. tickmarks..
axis.title=element_blank(), # .. axis labels..
panel.background = element_blank()) + # .. background gridlines
coord_equal() +
theme(legend.position = c(0.2, 0.7),legend.text=element_text(size=8))
return(plot.seccom)
}
#################################
# wrapper around plot per section communale
plot_scenario_all_cslscp_plots=function(CHW.positions, name_scenario){
my.CHW.positions=CHW.positions
my.CHW.positions$count=1
duplicatedCHW=aggregate((my.CHW.positions$count),
by= list(posx=my.CHW.positions$x,posy=my.CHW.positions$y), FUN=(sum))
names(duplicatedCHW)=c("x","y","count")
my.CHW.positions$count=NULL
my.CHW.positions=merge(my.CHW.positions,duplicatedCHW, all.x=TRUE )
my.CHW.positions$capacities=my.CHW.positions$my.list.capa.here/my.CHW.positions$count
plot.scenario.seccom=PlotScenarioSeccom(my.CHW.positions)
return(list("map_seccom"=plot.scenario.seccom))
}
SwissTPH/CHWplacement documentation built on March 10, 2023, 2:34 p.m.
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#################################
# plotting function from Emilie Pothin
PlotMap=function(img,NAMEfile="",shpFile,colormapDT,Title.legend="", myalpha=1, width_polygon=0.2){
shapefile_df <- fortify(shpFile)
r=as.data.frame(rasterToPoints(img))
names(r)[3]="z"
r$name=NAMEfile
r$z=cut(r$z,unique(c(0,as.numeric(as.character(colormapDT$value)))))
gg<-ggplot(r)+geom_tile(aes(x=x,y=y,fill=factor(as.numeric(z),levels=1:nrow(colormapDT))), alpha=myalpha)+
geom_path(data = shapefile_df,
aes(x = long, y = lat, group = group),
color = 'black',size=width_polygon)+
theme_void()+
coord_fixed()+
theme(panel.border = element_blank())+
scale_fill_manual(Title.legend,breaks=1:nrow(colormapDT),labels=as.character(colormapDT$label), values = as.character(colormapDT$color),drop = FALSE)
return(gg)
}
#################################
# formating scenario files
plot_scenario_all_cslscp=function(CHW.positions, name_scenario){
my.CHW.positions=CHW.positions
my.CHW.positions$count=1
duplicatedCHW=aggregate((my.CHW.positions$count),
by= list(posx=my.CHW.positions$x,posy=my.CHW.positions$y), FUN=(sum))
names(duplicatedCHW)=c("x","y","count")
my.CHW.positions$count=NULL
my.CHW.positions=merge(my.CHW.positions,duplicatedCHW, all.x=TRUE )
my.CHW.positions$capacities=my.CHW.positions$my.list.capa.here/my.CHW.positions$count
my.CHW.positions$scenario=name_scenario
return(my.CHW.positions)
}
plot_scenario_all_cslscp_new_names=function(CHW.positions, name_scenario){
my.CHW.positions=CHW.positions
my.CHW.positions$count=1
duplicatedCHW=aggregate((my.CHW.positions$count),
by= list(posx=my.CHW.positions$x,posy=my.CHW.positions$y), FUN=(sum))
names(duplicatedCHW)=c("x","y","count")
my.CHW.positions$count=NULL
my.CHW.positions=merge(my.CHW.positions,duplicatedCHW, all.x=TRUE )
my.CHW.positions$capacities=my.CHW.positions$capacity/my.CHW.positions$count
my.CHW.positions$scenario=name_scenario
return(my.CHW.positions)
}
#################################
# Plot summary file per department
plot_dpt_summary=function(mydpt){
list_dpt3=seccom.shp@data %>% select(NAME_1, ID_1, departement) %>%
unique %>%
mutate(ADM1NAME =gsub("grande", "grand",tolower(gsub(" ", "-", NAME_1))),
dpt =gsub(" ", "", NAME_1),
departement=gsub("Reste", "",gsub(" ", "",
ifelse(departement=="Aire metropolitaine", "AireMetro", departement))))
mydpt_id1=unique(list_dpt3$ID_1[list_dpt3$dpt == mydpt])
mydpt_ADM1NAME=unique(list_dpt3$ADM1NAME[list_dpt3$dpt %in% mydpt])
mydepart=unique(list_dpt3$departement[list_dpt3$dpt %in% mydpt])
my.shp.dpt=subset(seccom.shp, ID_1 == mydpt_id1)
population.dpt=mask(crop(population.haiti, my.shp.dpt), my.shp.dpt)
friction.dpt=mask(crop(friction, my.shp.dpt), my.shp.dpt)
urb.dpt=mask(crop(population.urb.hai.dummy, my.shp.dpt), my.shp.dpt)
access.dpt=mask(crop(access.raster.spa.CCS, my.shp.dpt), my.shp.dpt)
CHW.positions.scenario.dpt.scenarioA=CHW.positions.scenarioA.CSLCP %>% filter(dpt %in% mydepart)
CHW.positions.scenario.dpt.scenarioB=CHW.positions.scenarioB.CSLCP %>% filter(dpt %in% mydepart)
CHW.positions.scenario.dpt.scenarioC=CHW.positions.scenarioC.CSLCP %>% filter(dpt %in% mydepart)
CHW.positions.scenario.dpt.scenarioC2=CHW.positions.scenarioC2.CSLCP %>% filter(dpt %in% mydepart)
CCS.shp.dpt=subset(CCS.shp,ADM1NAME == mydpt_ADM1NAME & SOURCE !="MIS")
CCS.shp.dpt=spTransform(CCS.shp.dpt,newproj)
CCS.dpt=data.frame(CCS.shp.dpt@coords)
map.population.dpt<-PlotMap(population.dpt,Title.legend="Population \ndensity",shpFile=my.shp.dpt,colormapDT=colormapDT0)+theme(legend.key.size = unit(0.16, "in"))
#map.population.dpt
map.friction.dpt<-PlotMap(friction.dpt*1000,Title.legend="Minutes to \ncross 1km ",shpFile=my.shp.dpt,colormapDT=colormapDTb2)+theme(legend.key.size = unit(0.16, "in"))
map.friction.dpt
map.population.dpt_frame=plot_grid(map.population.dpt,labels = c("2.")) +theme(plot.background = element_rect(color = "black"))
#plot_pop_fric
map.friction.dpt_frame=plot_grid(map.friction.dpt,labels = c("3.")) +theme(plot.background = element_rect(color = "black"))
plot_pop_fric=plot_grid(map.population.dpt_frame,
map.friction.dpt_frame,labels = c("2.", "3."), ncol=2)
travel.time.dpt<-PlotMap(access.dpt,Title.legend="Walking time\nto CCS\n(minutes)\n ",shpFile=my.shp.dpt,colormapDT=colormapDTb, myalpha = 0.7)+
geom_point(data=CCS.dpt,aes(x=coords.x1,y=coords.x2, shape="CCS"),col="red")+scale_shape_manual(values=17, name="")
map.A=travel.time.dpt+
geom_point(data=CHW.positions.scenario.dpt.scenarioA,aes(x=x,y=y, group=seq_along(rank), size=count),shape=20,col="dodgerblue")+
labs(size="Number\nof CHWs")
map.B=travel.time.dpt+
geom_point(data=CHW.positions.scenario.dpt.scenarioB,aes(x=x,y=y, group=seq_along(rank), size=count),shape=20,col="dodgerblue")+
labs(size="Number\nof CHWs")
map.C=travel.time.dpt+
geom_point(data=CHW.positions.scenario.dpt.scenarioC,aes(x=x,y=y, group=seq_along(rank), size=count),shape=20,col="dodgerblue")+
labs(size="Number\nof CHWs")
map.C2=travel.time.dpt+
geom_point(data=CHW.positions.scenario.dpt.scenarioC2,aes(x=x,y=y, group=seq_along(rank), size=count),shape=20,col="dodgerblue")+
labs(size="Number\nof CHWs")
legend <- get_legend(map.A + theme(legend.box.margin = margin(0, 0, 0, 0), legend.position = "bottom")+
guides(size=guide_legend(order=2), fill=guide_legend(order=1)))
title <- ggdraw() + draw_label( " 1.", fontface = 'bold', x = 0, hjust = 0 ) + theme(plot.margin = margin(0, 0, 0, 0))
plot_scenarios=plot_grid(map.A+theme(legend.position = "none"),
map.B+theme(legend.position = "none"),
map.C+theme(legend.position = "none"),
map.C2+theme(legend.position = "none") ,
ncol=2, labels = c("A", "B", "C", "C2"))
plot_scenarios_title=plot_grid(title, plot_scenarios, ncol=1,rel_heights = c(0.05,1))
plot_scenarios_legend=plot_grid(plot_scenarios_title, legend, rel_heights = c(1, .1), ncol=1) +
theme(plot.background = element_rect(color = "black"))
#plot_scenarios_legend
all.dpt=plot_grid(plot_scenarios_legend,plot_pop_fric , ncol=1, scale=1,rel_heights = c(2.7,1))
#all.dpt
return(all.dpt)
}
#################################
# Plot gap per section communale
PlotGapScenarioSeccom=function(CHW.positions){
scenario.sp=SpatialPointsDataFrame(CHW.positions,
CHW.positions, #the R object to convert
proj4string = crs(newproj))
scenario.sp <- over(scenario.sp, seccom.shp)
CHW.per.seccom=data.frame(table(scenario.sp$ID_4)) ;names(CHW.per.seccom)=c("ID_4","nbCHW")
CHW.per.seccom=sp::merge(seccom.shp,CHW.per.seccom)
CHW.per.seccom=merge(CHW.per.seccom,spa.seccom,all=TRUE)
CHW.per.seccom@data$nbCHW[is.na(CHW.per.seccom@data$nbCHW)]=0
CHW.per.seccom@data$nbCHWSPA[is.na(CHW.per.seccom@data$nbCHWSPA)]=0
CHW.per.seccom@data$diffSPA=CHW.per.seccom@data$nbCHWSPA-CHW.per.seccom@data$nbCHW
CHW.per.seccom.df <- tidy(CHW.per.seccom)
CHW.per.seccom$polyID <- sapply(slot(CHW.per.seccom, "polygons"), function(x) slot(x, "ID"))
CHW.per.seccom.df <- merge(CHW.per.seccom.df, CHW.per.seccom, by.x = "id", by.y="polyID")
CHW.per.seccom.df$diffSPA.cut=cut(CHW.per.seccom.df$diffSPA, breaks=c(-350,-50,-10,0,10,50,300),
label=c("< -50","-50 to -10","-10 to 0","0 to 10","10 to 50", ">50"),include.lowest=TRUE, right=FALSE)
plot.seccom=ggplot() + # initialize ggplot object
geom_polygon( # make a polygon
data = CHW.per.seccom.df, # data frame
aes(x = long, y = lat, group = group, # coordinates, and group them by polygons
fill = diffSPA.cut)) + # variable to use for filling
#scale_fill_gradient2( name="difference",low="red", high="lightblue",mid="white") +
scale_fill_brewer( name="Difference\nin nb. of CHWs", type="seq", palette="RdBu", drop=FALSE)+
geom_path(data = seccom.shp.union,
aes(x = long, y = lat, group = group),
color = 'black',size=0.2)+
theme(line = element_blank(), # remove axis lines ..
axis.text=element_blank(), # .. tickmarks..
axis.title=element_blank(), # .. axis labels..
panel.background = element_blank(),
legend.key.size = unit(0.5, "cm"),
legend.position = c(0.2, 0.7),
legend.text=element_text(size=8),legend.title=element_text(size=10))+ # .. background gridlines
coord_equal()
return(list("plot"=plot.seccom, "file"=CHW.per.seccom@data))
}
#################################
# Plot total per section communale
PlotScenarioSeccom=function(CHW.positions){
scenario.sp=SpatialPointsDataFrame(CHW.positions[c("x","y")],
CHW.positions, #the R object to convert
proj4string = crs(newproj))
scenario.sp <- over(scenario.sp, seccom.shp)
CHW.per.seccom=data.frame(table(scenario.sp$ID_4)) ;names(CHW.per.seccom)=c("ID_4","nbCHW")
CHW.per.seccom=sp::merge(seccom.shp,CHW.per.seccom)
CHW.per.seccom.df <- tidy(CHW.per.seccom)
CHW.per.seccom$polyID <- sapply(slot(CHW.per.seccom, "polygons"), function(x) slot(x, "ID"))
CHW.per.seccom.df <- merge(CHW.per.seccom.df, CHW.per.seccom, by.x = "id", by.y="polyID")
CHW.per.seccom.df$nbCHW[is.na(CHW.per.seccom.df$nbCHW)]=0
CHW.per.seccom.df$nbCHW.cut=cut(CHW.per.seccom.df$nbCHW, breaks=c(0,10,20,30,40,50,500),
label=c("<10","10 to 20","20 to 30","30 to 40","40 to 50", ">50"), include.lowest=TRUE, right=TRUE)
print(max(CHW.per.seccom.df$nbCHW))
plot.seccom=ggplot() + # initialize ggplot object
geom_polygon( # make a polygon
data = CHW.per.seccom.df, # data frame
aes(x = long, y = lat, group = group, # coordinates, and group them by polygons
fill = nbCHW.cut)) + # variable to use for filling
scale_fill_brewer( name="Nb. of CHWs", type="seq", palette="Reds", drop=FALSE)+
geom_path(data = seccom.shp.union,
aes(x = long, y = lat, group = group),
color = 'black',size=0.2)+
theme(line = element_blank(), # remove axis lines ..
axis.text=element_blank(), # .. tickmarks..
axis.title=element_blank(), # .. axis labels..
panel.background = element_blank()) + # .. background gridlines
coord_equal() +
theme(legend.position = c(0.2, 0.7),legend.text=element_text(size=8))
return(plot.seccom)
}
#################################
# wrapper around plot per section communale
plot_scenario_all_cslscp_plots=function(CHW.positions, name_scenario){
my.CHW.positions=CHW.positions
my.CHW.positions$count=1
duplicatedCHW=aggregate((my.CHW.positions$count),
by= list(posx=my.CHW.positions$x,posy=my.CHW.positions$y), FUN=(sum))
names(duplicatedCHW)=c("x","y","count")
my.CHW.positions$count=NULL
my.CHW.positions=merge(my.CHW.positions,duplicatedCHW, all.x=TRUE )
my.CHW.positions$capacities=my.CHW.positions$my.list.capa.here/my.CHW.positions$count
plot.scenario.seccom=PlotScenarioSeccom(my.CHW.positions)
return(list("map_seccom"=plot.scenario.seccom))
}
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