How to turn the color scale in Plotly r to log scale

Question

I am trying to have a logarithmic scale for the color bar in R, any ideas on how I can do it?

My code:

TEST_DATAFRAME = read.table(TEST_FILE, sep="\t",skip=2, header=T)
PROD_DATAFRAME = read.table(PROD_FILE, sep="\t",skip=2, header=T)

PARAMETER = "Vf_High"
LST_RESIDUAL <- PROD_DATAFRAME[PARAMETER] - TEST_DATAFRAME[PARAMETER]
PARAM_DATAFRAME <- data.frame("NEW_MEASUREMENT" = TEST_DATAFRAME[PARAMETER], 
                              "OLD_MEASUREMENT" = PROD_DATAFRAME[PARAMETER], 
                              "RESIDUAL" = LST_RESIDUAL)

colnames(PARAM_DATAFRAME) <- c("NEW_MEASUREMENT","OLD_MEASUREMENT","RESIDUAL")

p <- plot_ly(PARAM_DATAFRAME, x = ~OLD_MEASUREMENT, y = ~NEW_MEASUREMENT, color=~RESIDUAL,  colorscale = "Log",
             hovertext = paste("<b>New Measurement :</b>", PARAM_DATAFRAME$NEW_MEASUREMENT,
                               "<br><b>Old Measurement :</b>", PARAM_DATAFRAME$OLD_MEASUREMENT,
                               "<br><b>Residual :</b>" , PARAM_DATAFRAME$RESIDUAL)) %>% add_markers()

#p <- layout(p, color = list(type = "log"))
p

this is my current output:

I also tried the following code:

TEST_DATAFRAME = read.table(TEST_FILE, sep="\t",skip=2, header=T)
PROD_DATAFRAME = read.table(PROD_FILE, sep="\t",skip=2, header=T)

PARAMETER = "Vf_High"
LST_RESIDUAL <- PROD_DATAFRAME[PARAMETER] - TEST_DATAFRAME[PARAMETER]
PARAM_DATAFRAME <- data.frame("NEW_MEASUREMENT" = TEST_DATAFRAME[PARAMETER], 
                              "OLD_MEASUREMENT" = PROD_DATAFRAME[PARAMETER], 
                              "RESIDUAL" = abs(LST_RESIDUAL))

colnames(PARAM_DATAFRAME) <- c("NEW_MEASUREMENT","OLD_MEASUREMENT","RESIDUAL")

brks <- pretty(range(PARAM_DATAFRAME$RESIDUAL))
gg <- ggplot(PARAM_DATAFRAME, aes(NEW_MEASUREMENT, OLD_MEASUREMENT, color = RESIDUAL)) +
  geom_point() +
  scale_colour_gradient(
    low = "blue", high = "red",
    trans = "log", breaks = brks, labels = brks) +
  theme_minimal()

ggplotly(gg)

this is the result:

How can I give it legible labelling? I want to configure the color bar as the following:

Maurits Evers · Accepted Answer · 2021-12-21T02:06:03.207

3

You could use ggplot to generate the logarithmic colour scale and then have plotly::ggplotly turn the ggplot grob into a plotly object.

Since you don't provide reproducible sample data, here is an example based on mtcars

brks <- pretty(range(mtcars$disp))
gg <- ggplot(mtcars, aes(mpg, wt, colour = disp)) +
    geom_point() +
    scale_colour_gradient(
        low = "blue", high = "red",
        trans = "log", breaks = brks, labels = brks) +
    theme_minimal()

ggplotly(gg)

Update

In response to your comment, here is a minimal reproducible example.

First we generate some sample data

set.seed(2018)
df <- data.frame(
    x = 1:100,
    y = 1:100 + rnorm(100),
    val = 10^seq(-5, 2, length.out = 100))

We then define suitable breaks

brks <- 10^seq(floor(log10(min(df$val))), ceiling(log10(max(df$val))), by = 1)

Generate ggplot grob

gg <- ggplot(df, aes(x, y, colour = val)) +
    geom_point() +
    scale_colour_gradient(
        low = "blue", high = "red",
        trans = "log",
        breaks = brks,
        labels = brks) +
    theme_minimal()

Finally show as plotly object

ggplotly(gg)

Without using `ggplotly`

To achieve the same without the ggplotly detour, use the colorbar argument within marker to define tick spacings and labels.

# Determine range of log10-scale
rg <- range(log10(df$val))

# Plot
plot_ly(
    df, 
    x = ~x, y = ~y, 
    type = "scatter",
    mode = "markers",
    marker = list(
        color = ~log10(val),
        colorbar = list(
            tickmode = "array",
            ticktext = 10^seq(floor(rg[1]), ceiling(rg[2])),
            tickvals = seq(floor(rg[1]), ceiling(rg[2])))))

edited Dec 21 '21 at 02:06

answered Nov 29 '19 at 04:31

Maurits Evers

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I modified my answer, please review – Adhil Nov 29 '19 at 06:04
1

@Adhil Not clear what you're asking. Please make your example reproducible by including [minimal & reproducible data & code](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example). We don't have access to either of those files, so don't have anything concrete to work with. – Maurits Evers Nov 29 '19 at 06:05
its a quite large Test Data file, most of the RESIDUALS are between 0 -0.01, however there are outlier residuals between 1 and 2, i want to show that in the color scale, however, i have difficulty implementing a logarithmic scale on the colour bar, the code you gave me works well, however, number labelling on the color bar is not clear, anyway I can clean it up? – Adhil Nov 29 '19 at 06:23
@Adhil So what kind of labels do you want? That shouldn’t be difficult to implement by specifying appropriate breaks. Can you give me some concrete numbers? – Maurits Evers Nov 29 '19 at 09:09
please refer to my updated query I have mentioned how I want the color bar to look. – Adhil Dec 02 '19 at 10:31
How to do this directly in plotly without ggplot? – kosk Dec 20 '21 at 12:44
1

@kosk Please see my latest edit. – Maurits Evers Dec 21 '21 at 02:06
Mauritis Evers, thank you. Is it possible to apply somehow this solution of yours for log to log and/sqrt transformation on a plotly map that I mention here: https://stackoverflow.com/questions/70404498/r-plotly-maping-issue ? Is it possible to sqrt/log transform somehow colors on a map but to keep the original values on the color-bar? Thanks – kosk Dec 21 '21 at 08:33
1

@kosk Yes I'm pretty sure that shouldn't be too difficult. I had a look at your post but it's missing some representative sample data. Without sample data it's difficult to demonstrate with a concrete example. – Maurits Evers Dec 21 '21 at 11:30
@MauritsEvers Here is the mock data with pretty much same issue if you could help: https://stackoverflow.com/questions/70415844/how-to-log-transform-values-for-color-in-plotly-but-to-keep-original-values-on-c?noredirect=1#comment124494859_70415844 – kosk Dec 21 '21 at 12:54
@kosk Agreed, this is exactly the same issue. I've posted an answer [here](https://stackoverflow.com/a/70443652/6530970). – Maurits Evers Dec 22 '21 at 02:33

How to turn the color scale in Plotly r to log scale

1 Answers1

Update

Without using `ggplotly`

Linked

How to turn the color scale in Plotly r to log scale

1 Answers1

Update

Without using ggplotly

Linked

Without using `ggplotly`