Problem with setting number of colours showing using scale_fill_gradientn and guide

Ka Ming Fung

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Jan 24, 2018, 5:52:08 AM1/24/18

to ggplot2

Hey guys,

I have a data frame with a list of lon, lat and continuous values. I want to make the color bar with 6 colors like this:

So I tried the following codes:

scale_fill_gradientn(colours = rev(colorRampPalette(brewer.pal(11,"RdBu"))(11)[6:11],
breaks = data.breaks

guide = guide_colorbar(title = legend.unit,
nbin = 6, raster = F))

But what I got is a color bar with 7 color, like this,

Would you please advise how I could get a color bar with 6 colors?

Thanks a lot. It has been troubled me for a long time and my temporary solution is to transform the continuous data to some discrete values and plot them with discrete color legend.

Regards,

fkm

Adriano Fantini

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Jan 24, 2018, 6:01:03 AM1/24/18

to Ka Ming Fung, ggplot2

You seem to be using continuous values, you should definitely factorize those values if you want a discrete scale, that 's what ggplot expects of you at least. So cut them with cut, and assign a label to each bin... something along these lines:

https://stackoverflow.com/questions/28217146/how-to-shift-legend-for-discrete-scales-in-ggplot

Adriano Fantini

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FUNG, Ka Ming

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Jan 24, 2018, 9:25:55 AM1/24/18

to Adriano Fantini, ggplot2

Dear Adriano,

I would like to have a continuous scale with specified number of color.

Thanks for your suggestions. I am using the same method as a temporary solution to create the “color bar” I want. I wonder if there is right way to set the number of colors (aka nbin?) in ggplot2, so that my setting won’t get overrided.

Regards,

Fkm

On Wed, 24 Jan 2018 at 06:00, Adriano Fantini <adr.f...@gmail.com> wrote:

You seem to be using continuous values, you should definitely factorize those values if you want a discrete scale, that 's what ggplot expects of you at least. So cut them with cut, and assign a label to each bin... something along these lines:
https://stackoverflow.com/questions/28217146/how-to-shift-legend-for-discrete-scales-in-ggplot

Adriano Fantini

2018-01-24 6:49 GMT+01:00 Ka Ming Fung <fkm...@gmail.com>:
Hey guys,

I have a data frame with a list of lon, lat and continuous values. I want to make the color bar with 6 colors like this:

So I tried the following codes:

scale_fill_gradientn(colours = rev(colorRampPalette(brewer.pal(11,"RdBu"))(11)[6:11],
breaks = data.breaks
guide = guide_colorbar(title = legend.unit,
nbin = 6, raster = F))

But what I got is a color bar with 7 color, like this,

Would you please advise how I could get a color bar with 6 colors?

Thanks a lot. It has been troubled me for a long time and my temporary solution is to transform the continuous data to some discrete values and plot them with discrete color legend.

Regards,
fkm

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Adriano Fantini

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Jan 24, 2018, 10:48:49 AM1/24/18

to FUNG, Ka Ming, ggplot2

I do not understand what you mean with "a continuous scale with specified number of color". Looks like a discrete scale to me. The scale you showed in the first list looks discrete as well.

Cheers,

AF

Adriano Fantini

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FUNG, Ka Ming

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Jan 24, 2018, 10:58:08 AM1/24/18

to Adriano Fantini, ggplot2

Dear Adriano,

The first figure I showed is a discrete scale, but I want to make a continuous scale that looks like a discrete one. It is because, for a heat map like the one below (from Saikawa et al. (2013)), readers would find it easier to associate colors on grids on the map with color and values in the scale bar, than with a continuous color scale with many shades of colors.

I hope it helps to explain my motive for looking for a way to control the number of shades of colors precisely in a color bar.

Thanks,

fkm

Adriano Fantini

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Jan 25, 2018, 4:04:55 AM1/25/18

to FUNG, Ka Ming, ggplot2

I would argue that the one you just showed is not a continuous scale that looks like a discrete one but quite the opposite: a discrete scales with values so close that it looks like a continuous one. I think that's the way you should approach this. If you however insist in trying to use a continuous scale: can you provide your dataset, or an example dataset, so that one can test?

Adriano Fantini

FUNG, Ka Ming

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Jan 25, 2018, 1:39:13 PM1/25/18

to Adriano Fantini, ggplot2

Dear Adriano,

Thank you for your reply. Anyway, what I wonder is if there is a way to restrict the number of colors used in a colorbar of ggplot2. Attached please find my sample codes, data, and plots for your testing.

Thanks again for your patience and help.

Regards,

fkm

sample_code.R

sample_data.RDS

Brandon Hurr

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Jan 25, 2018, 2:23:33 PM1/25/18

to FUNG, Ka Ming, Adriano Fantini, ggplot2

What version are you using?

I get 11 colors.
Inline image 2

ggplot(data = plot.data, mapping = aes(x = lon, y = lat)) +
    coord_fixed(expand = FALSE) +
    theme(legend.justification = c(0,0.5),
              legend.text.align = 1) +
    geom_raster(aes(fill = value), interpolate = F) +
    scale_fill_gradientn(colors = rev(colorRampPalette(brewer.pal(11,"RdBu"))(11)),
                               na.value = NA,
                               breaks = data.labs,
                               limits = c(-zlim, zlim),
                               guide = guide_colorbar(title = "11 Bars?",
                                                      raster = FALSE,
                                                      nbin = 11)
                               )

> devtools::session_info()
Session info -------------------------------------------------------------------------------------------------
setting value
version R version 3.4.2 (2017-09-28)
system   x86_64, darwin15.6.0
ui       AQUA
language (EN)
collate en_US.UTF-8
tz       America/Los_Angeles
date     2018-01-25

Packages -----------------------------------------------------------------------------------------------------
package      * version    date       source
assertthat     0.2.0      2017-04-11 CRAN (R 3.4.0)
base         * 3.4.2      2017-10-04 local
bindr          0.1        2016-11-13 cran (@0.1)
bindrcpp       0.2        2017-06-17 cran (@0.2)
colorspace     1.3-2      2016-12-14 CRAN (R 3.4.0)
compiler       3.4.2      2017-10-04 local
datasets     * 3.4.2      2017-10-04 local
devtools       1.13.0     2017-05-08 CRAN (R 3.4.0)
digest         0.6.13     2017-12-14 cran (@0.6.13)
dplyr          0.7.4.9000 2018-01-15 Github (tidyverse/dplyr@f49115b)
ggplot2      * 2.2.1.9000 2018-01-15 Github (tidyverse/ggplot2@bf9255e)
ggpubr       * 0.1.6      2017-11-14 CRAN (R 3.4.2)
glue           1.2.0      2017-10-29 cran (@1.2.0)
graphics     * 3.4.2      2017-10-04 local
grDevices    * 3.4.2      2017-10-04 local
grid           3.4.2      2017-10-04 local
gtable         0.2.0      2016-02-26 CRAN (R 3.4.0)
labeling       0.3        2014-08-23 CRAN (R 3.4.0)
lazyeval       0.2.1      2017-10-29 cran (@0.2.1)
magrittr     * 1.5        2014-11-22 CRAN (R 3.4.0)
memoise        1.1.0      2017-04-21 CRAN (R 3.4.0)
methods      * 3.4.2      2017-10-04 local
munsell        0.4.3      2016-02-13 CRAN (R 3.4.0)
pkgconfig      2.0.1      2017-03-21 cran (@2.0.1)
plyr           1.8.4      2016-06-08 CRAN (R 3.4.0)
purrr          0.2.4.9000 2017-11-28 Github (tidyverse/purrr@62b135a)
R6             2.2.2      2017-06-17 cran (@2.2.2)
RColorBrewer * 1.1-2      2014-12-07 CRAN (R 3.4.0)
Rcpp           0.12.14    2017-11-23 cran (@0.12.14)
rlang          0.1.6.9003 2018-01-15 Github (tidyverse/rlang@e41652d)
scales         0.5.0.9000 2017-10-10 Github (hadley/scales@d767915)
stats        * 3.4.2      2017-10-04 local
tibble         1.3.4      2017-08-22 cran (@1.3.4)
tidyselect     0.2.3      2017-11-06 cran (@0.2.3)
tools          3.4.2      2017-10-04 local
utils        * 3.4.2      2017-10-04 local
withr          2.1.1.9000 2018-01-15 Github (jimhester/withr@df18523)

FUNG, Ka Ming

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Jan 25, 2018, 2:38:18 PM1/25/18

to Brandon Hurr, Adriano Fantini, ggplot2

Dear Brandon,

Still 9 colors only after updating all packages. Here comes my session info. Thanks.

> devtools::session_info()

Session info ---------------------------------------------------------------------------------------------------

setting value

version R version 3.4.3 (2017-11-30)

system x86_64, darwin15.6.0

ui RStudio (1.1.383)

language (EN)

collate en_US.UTF-8

tz America/New_York

date 2018-01-25

Packages -------------------------------------------------------------------------------------------------------

package * version date source

assertthat 0.2.0 2017-04-11 CRAN (R 3.4.0)

base * 3.4.3 2017-12-07 local

bindr 0.1 2016-11-13 CRAN (R 3.4.0)

bindrcpp 0.2 2017-06-17 CRAN (R 3.4.0)

broom 0.4.3 2017-11-20 CRAN (R 3.4.3)

cellranger 1.1.0 2016-07-27 CRAN (R 3.4.0)

cli 1.0.0 2017-11-05 CRAN (R 3.4.2)

colorspace 1.3-2 2016-12-14 CRAN (R 3.4.0)

compiler 3.4.3 2017-12-07 local

cowplot 0.9.2 2017-12-17 CRAN (R 3.4.3)

crayon 1.3.4 2017-09-16 CRAN (R 3.4.1)

datasets * 3.4.3 2017-12-07 local

devtools 1.13.4 2017-11-09 CRAN (R 3.4.2)

digest 0.6.14 2018-01-14 CRAN (R 3.4.3)

dplyr * 0.7.4 2017-09-28 CRAN (R 3.4.2)

forcats * 0.2.0 2017-01-23 CRAN (R 3.4.0)

foreign 0.8-69 2017-06-22 CRAN (R 3.4.3)

ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.4.0)

ggpubr * 0.1.6 2017-11-14 CRAN (R 3.4.2)

glue 1.2.0 2017-10-29 CRAN (R 3.4.2)

graphics * 3.4.3 2017-12-07 local

grDevices * 3.4.3 2017-12-07 local

grid 3.4.3 2017-12-07 local

gtable 0.2.0 2016-02-26 CRAN (R 3.4.0)

haven 1.1.1 2018-01-18 CRAN (R 3.4.3)

hms 0.4.1 2018-01-24 CRAN (R 3.4.3)

httr 1.3.1 2017-08-20 CRAN (R 3.4.1)

jsonlite 1.5 2017-06-01 CRAN (R 3.4.0)

labeling 0.3 2014-08-23 CRAN (R 3.4.0)

lattice 0.20-35 2017-03-25 CRAN (R 3.4.3)

lazyeval 0.2.1 2017-10-29 CRAN (R 3.4.2)

lubridate 1.7.1 2017-11-03 CRAN (R 3.4.2)

magrittr * 1.5 2014-11-22 CRAN (R 3.4.0)

maps * 3.2.0 2017-06-08 CRAN (R 3.4.0)

memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)

methods * 3.4.3 2017-12-07 local

mnormt 1.5-5 2016-10-15 CRAN (R 3.4.0)

modelr 0.1.1 2017-07-24 CRAN (R 3.4.1)

munsell 0.4.3 2016-02-13 CRAN (R 3.4.0)

nlme 3.1-131 2017-02-06 CRAN (R 3.4.3)

parallel 3.4.3 2017-12-07 local

pillar 1.1.0 2018-01-14 CRAN (R 3.4.3)

pkgconfig 2.0.1 2017-03-21 CRAN (R 3.4.0)

plyr 1.8.4 2016-06-08 CRAN (R 3.4.0)

psych 1.7.8 2017-09-09 CRAN (R 3.4.3)

purrr * 0.2.4 2017-10-18 CRAN (R 3.4.2)

R6 2.2.2 2017-06-17 CRAN (R 3.4.0)

RColorBrewer * 1.1-2 2014-12-07 CRAN (R 3.4.0)

Rcpp 0.12.15 2018-01-20 CRAN (R 3.4.3)

readr * 1.1.1 2017-05-16 CRAN (R 3.4.0)

readxl 1.0.0 2017-04-18 CRAN (R 3.4.0)

reshape2 1.4.3 2017-12-11 CRAN (R 3.4.3)

rlang 0.1.6 2017-12-21 CRAN (R 3.4.3)

rstudioapi 0.7 2017-09-07 CRAN (R 3.4.1)

rvest 0.3.2 2016-06-17 CRAN (R 3.4.0)

scales 0.5.0 2017-08-24 CRAN (R 3.4.1)

stats * 3.4.3 2017-12-07 local

stringi 1.1.6 2017-11-17 CRAN (R 3.4.2)

stringr * 1.2.0 2017-02-18 CRAN (R 3.4.0)

tibble * 1.4.2 2018-01-22 CRAN (R 3.4.3)

tidyr * 0.7.2 2017-10-16 CRAN (R 3.4.2)

tidyverse * 1.2.1 2017-11-14 CRAN (R 3.4.2)

tools 3.4.3 2017-12-07 local

utils * 3.4.3 2017-12-07 local

withr 2.1.1 2017-12-19 CRAN (R 3.4.3)

xml2 1.2.0 2018-01-24 CRAN (R 3.4.3)

yaml 2.1.16 2017-12-12 CRAN (R 3.4.3)

Regards,

fkm

Brandon Hurr

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Jan 25, 2018, 2:41:34 PM1/25/18

to FUNG, Ka Ming, Adriano Fantini, ggplot2

maybe try this:

devtools::dev_mode()

devtools::install_github("tidyverse/ggplot2")

This should put you into development mode. Install a github version of ggplot2 and maybe a few other packages that are new.

Then try replotting. See if it's something that was fixed very recently.

If it still doesn't work, I'm at a loss.

B

FUNG, Ka Ming

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Jan 25, 2018, 3:06:18 PM1/25/18

to Brandon Hurr, Adriano Fantini, ggplot2

Dear Brandon,

I got 11 colors now. Thank you so much for all of your replies.

I followed the method mentioned here at https://gist.github.com/kohske/1150934 to install the dev version of ggplot2.

Problem with setting number of colours showing using scale_fill_gradientn and guide_colorbar

Ka Ming Fung

Adriano Fantini

FUNG, Ka Ming

Adriano Fantini

FUNG, Ka Ming

Adriano Fantini

FUNG, Ka Ming

Brandon Hurr

FUNG, Ka Ming

Brandon Hurr

FUNG, Ka Ming