Please allow geom_GeomRrect() to be implemented in plotly. Thank you!!

Please briefly describe your problem and what output you expect. If you have a question, please don't use this form, but instead ask on the community forum http://community.plot.ly/c/api/r or stackoverflow http://stackoverflow.com.

Please include a minimal reprex. The goal of a reprex is to make it as easy as possible for me to recreate your problem so that I can fix it. If you've never heard of a reprex before, start by reading https://github.com/tidyverse/reprex#readme, and follow the advice further down the page. Do NOT include session info unless it's explicitly asked for, or you've used reprex::reprex(..., si = TRUE) to hide it away.

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Brief description of the problem

# insert reprex here

Where is geom_GeomRrec() from? Can you give an example?

Hi Carson, sure.

library(ggplot2)
library(devtools)
devtools::install_github("hrbrmstr/statebins")
library(statebins)



#################################
### CHROMOSOME DETAILS - HG19 ###
#################################

# hg19 chromosome sizes
chrom_sizes <- structure(list(chromosome = c("M", "1", "2", "3", "4", 
                                          "5", "6", "7", "8", "9", "10", "11", "12", 
                                          "13", "14", "15", "16", "17", "18", "19", 
                                          "20", "21", "22", "X", "Y"), 
                              size = c(16571L, 249250621L, 
                                       243199373L, 198022430L, 191154276L, 180915260L, 171115067L, 159138663L, 
                                       146364022L, 141213431L, 135534747L, 135006516L, 133851895L, 115169878L, 
                                       107349540L, 102531392L, 90354753L, 81195210L, 78077248L, 59128983L, 
                                       63025520L, 48129895L, 51304566L, 155270560L, 59373566L)), 
                         .Names = c("chromosome", "size"), class = "data.frame", row.names = c(NA, -25L))

# hg19 centromere locations
centromeres <- structure(list(chromosome = c("1", "2", "3", "4", 
                                          "5", "6", "7", "8", "9", "X", "Y", "10", 
                                          "11", "12", "13", "14", "15", "16", "17", 
                                          "18", "19", "20", "21", "22"), 
                              start = c(121535434L, 
                                        92326171L, 90504854L, 49660117L, 46405641L, 58830166L, 58054331L, 
                                        43838887L, 47367679L, 58632012L, 10104553L, 39254935L, 51644205L, 
                                        34856694L, 16000000L, 16000000L, 17000000L, 35335801L, 22263006L, 
                                        15460898L, 24681782L, 26369569L, 11288129L, 13000000L), 
                              end = c(124535434L, 
                                      95326171L, 93504854L, 52660117L, 49405641L, 61830166L, 61054331L, 
                                      46838887L, 50367679L, 61632012L, 13104553L, 42254935L, 54644205L, 
                                      37856694L, 19000000L, 19000000L, 20000000L, 38335801L, 25263006L, 
                                      18460898L, 27681782L, 29369569L, 14288129L, 16000000L)), 
                         .Names = c("chromosome", "start", "end"), class = "data.frame", row.names = c(NA, -24L))

# create an ordered factor level to use for the chromosomes in all the datasets
chrom_order <- c("1","2","3","4","5","6","7","8","9","10",
                 "11","12","13","14","15","16","17","18","19",
                 "20","21","22","X","Y","M")
chrom_key <- setNames(object = as.character(c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 
                                              12, 13, 14, 15, 16, 17, 18, 19, 20, 
                                              21, 22, 23, 24, 25)), nm = chrom_order)
chrom_order <- factor(x = chrom_order, levels = chrom_order)

# convert the chromosome column in each dataset to the ordered factor
centromeres$mid <- (centromeres$end - centromeres$start) / 2 + centromeres$start
chrom_sizes <- chrom_sizes[-which(chrom_sizes$chromosome %in% c("X","Y","M")),]
centromeres <- centromeres[-which(centromeres$chromosome %in% c("X","Y","M")),]
chrom_key <- chrom_key[-which(chrom_key %in% c("23","24","25"))]
chrom_order <- as.factor(as.character(chrom_order[-which(chrom_order %in% c("X","Y","M"))]))
chrom_sizes <- data.frame(chromosome=chrom_sizes$chromosome, start=0, mid=centromeres$mid, end=chrom_sizes$size)
chrom_sizes[["chromosome"]] <- factor(x = chrom_sizes[["chromosome"]], levels = chrom_order)
centromeres[["chromosome"]] <- factor(x = centromeres[["chromosome"]], levels = chrom_order)
chrom_sizes$start <- chrom_sizes$start/10^6
chrom_sizes$mid <- chrom_sizes$mid/10^6
chrom_sizes$end <- chrom_sizes$end/10^6
centromeres$start <- centromeres$start/10^6
centromeres$end <- centromeres$end/10^6
centromeres$mid <- centromeres$mid/10^6



############
### PLOT ###
############

arm1 <- data.frame(chromosome=chrom_sizes$chromosome, start=chrom_sizes$start, end=chrom_sizes$mid)
arm2 <- data.frame(chromosome=chrom_sizes$chromosome, start=chrom_sizes$mid, end=chrom_sizes$end)
data1 <- data2 <- rbind(arm1, arm2)
data1$pop <- sample(c("Pop1","Pop2","Pop3","Pop4","Pop5"), nrow(data1), replace=T)
data2$pop <- sample(c("Pop1","Pop2","Pop3","Pop4","Pop5"), nrow(data2), replace=T)

plot <- ggplot(data = data1, aes(group = pop, fill = pop)) + 
  statebins:::geom_rrect(data = data1, aes(xmin = as.numeric(chromosome) - 0.4,
                                             xmax = as.numeric(chromosome) - 0,
                                             ymax = end, ymin = start, fill=pop)) +
  statebins:::geom_rrect(data = data2, aes(xmin = as.numeric(chromosome) + 0,
                                             xmax = as.numeric(chromosome) + 0.4,
                                             ymax = end, ymin = start, fill=pop)) +
  statebins:::geom_rrect(data=chrom_sizes, aes(xmin = as.numeric(chromosome) - 0.4, 
                                               xmax = as.numeric(chromosome) - 0, 
                                               ymax = mid, ymin = start), 
                         colour="black", fill = NA) + 
  statebins:::geom_rrect(data=chrom_sizes, aes(xmin = as.numeric(chromosome) + 0, 
                                               xmax = as.numeric(chromosome) + 0.4, 
                                               ymax = mid, ymin = start), 
                         colour="black", fill = NA) +
  statebins:::geom_rrect(data=chrom_sizes, aes(xmin = as.numeric(chromosome) - 0.4, 
                                               xmax = as.numeric(chromosome) - 0, 
                                               ymax = end, ymin = mid), 
                         colour="black", fill = NA) + 
  statebins:::geom_rrect(data=chrom_sizes, aes(xmin = as.numeric(chromosome) + 0, 
                                               xmax = as.numeric(chromosome) + 0.4, 
                                               ymax = end, ymin = mid), 
                         colour="black", fill = NA) +
  scale_x_discrete(name = "Chromosome", limits=c(1:22), expand=c(0.01,0.01), drop=FALSE) +
  scale_fill_manual(values = rainbow(5)) +
  scale_y_continuous(expand=c(0.03,0.03)) +
  theme(axis.text.x = element_text(colour = "black"), 
        panel.grid.major = element_blank(), 
        panel.grid.minor = element_blank(), 
        panel.background = element_blank(),
        axis.ticks = element_blank(),
        plot.title = element_text(hjust = 0.5, face="bold"),
        plot.subtitle = element_text(hjust = 0.5),
        legend.text = element_text(family="Courier")) + 
  guides(fill=guide_legend(title="Population")) +
  ylab("Position (Mb)")
print(plot)

##############
### PLOTLY ###
##############

library(plotly)
ggplotly(plot, tooltip = c("pop"))

In geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]],  ... :
                      geom_GeomRrect() has yet to be implemented in plotly.
                      If you'd like to see this geom implemented,
                      Please open an issue with your example code at
                      https://github.com/ropensci/plotly/issues

Thanks, added to #566

Thanks, I downloaded the updated version (4.9) but get the same warning and no output:

library(plotly)
ggplotly(plot, tooltip = c("pop"))

In geom2trace.default(dots[[1L]][[5L]], dots[[2L]][[1L]], dots[[3L]][[1L]]) :
  geom_GeomRrect() has yet to be implemented in plotly.
  If you'd like to see this geom implemented,
  Please open an issue with your example code at
  https://github.com/ropensci/plotly/issues

Oh, it's not implemented, I just made a note to do it sometime in the future

Ah, roger. Thanks.

commeting so it can be revived!

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Please allow geom_GeomRrect() to be implemented in plotly. Thank you!! #1558

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Please allow geom_GeomRrect() to be implemented in plotly. Thank you!! #1558

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cpsievert commented on Jul 1, 2019

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