How to plot positions along a chromosome graphic

Question

I would like to generate a plot depicting 14 linear chromosomes for the organism I work on, to scale, with coloured bars at specified locations along each chromosome. Ideally I\

Answer 1

data

{ # dataframes
  dfChrSize<-read.table(text="chrName           chrSize
         1         640851
         2         947102
         3        1067971
         4        1200490
         5        1343557
         6        1418242
         7        1445207
         8        1472805
         9        1541735
        10        1687656
        11        2038340
        12        2271494
        13        2925236
        14        3291936", header=T)

  dfMarkPos<-read.table(text="chrName   markPos markSize markName
3          817702 50000 type1
12         1556936  50000 type2
13         1131566  50000 type2", header=T, stringsAsFactors=F)
}

idiogramFISH plot

install.packages("idiogramFISH")
library(idiogramFISH) # v. 1.16.1

par(mar=c(0,0,0,0) ) # b l t r

plotIdiograms(dfChrSize,dfMarkPos=dfMarkPos, 
              karIndex = FALSE,  
              karHeight = 4,
              orderChr = "original",
              chrWidth = .2, 
              chrSpacing = .5,
              legendHeight = 2,
              chromatids = FALSE,
              rulerIntervalMb = 1000000,
              useMinorTicks = TRUE,   # ruler 
              xlimLeftMod = 2,        # modify left margin
              ylimBotMod = -3,        # modify bottom margin
              classMbName = "",       # chr. title
              yPosRulerTitle = 3,     # ruler title pos.
              xPosRulerTitle = 3)

idiogramFISH coord. + ggplot

chrAndMarksMap <- mapGGChrMark(dfChrSize,dfMarkPos,chrSpacing = .8)

# ggplot

library(ggplot2)

ggplot() + 
  geom_polygon(aes(x=x,y=y,
                   group=Chr) 
               ,data=chrAndMarksMap$dataChr
               ,color="gray"
               ,fill="gray"
  ) +
  geom_polygon(aes(x=x,y=y,
                   group=id,
                   color=markName,
                   fill=markName) 
               ,data=chrAndMarksMap$dataMark
  ) +
  theme_classic()+
  scale_x_continuous(breaks=seq(1,nrow(dfChrSize),1)
  ) +
  scale_y_continuous(breaks = seq(0,3500000,500000),
                     labels = seq(0,3.5 , .5)
  ) +
  geom_segment(aes(y=0,yend=3500000,x=-Inf,xend=-Inf)
  )+
  theme(axis.line=element_blank(),
        axis.ticks.x = element_blank(),
        axis.title.x = element_blank(),
        axis.title.y = element_text(angle=0),
        legend.title = element_blank()
        ) +
  ylab("Mb")