# NIBR data analysis

**URL:** <https://discourse.pumas.ai/t/nibr-data-analysis/630>\
**Category:** How-to\
**Created:** [February 22, 2022, 11:56pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630 "2022-02-22T23:56:46Z")\
**Posts on this page:** 20\
**Page:** 2

<div class="post-metadata">

**Author:** ![julius](https://avatars.discourse-cdn.com/v4/letter/j/ecd19e/32.png) [@julius](https://discourse.pumas.ai/u/julius)\
**Post date:** [February 24, 2022, 10:04am UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/21 "2022-02-24T10:04:35Z")

</div>

Regarding the log ticks:  
Currently, Makie calculates log ticks the same way that it calculates normal ticks, just inside the log transformed range of values. That’s why you can get ticks like `10^0.5` as `0.5` is usually a nice tick value to have. If, however, you want only integer values, here’s a simple way to get that, which might at some point be a built-in option in Makie:

```nohighlight
# make a new placeholder type
struct IntegerTicks end

# integer ticks are just all integers within the axis limits
# (this should work ok if there's only a couple orders of magnitude, otherwise one would want to reduce the number of ticks)
MakieLayout.get_tickvalues(::IntegerTicks, vmin, vmax) = ceil(Int, vmin) : floor(Int, vmax)

f = Figure(resolution = (900, 600))

for (i, x) in enumerate([0.01, 0.001, 0.0001])
    lines(
        f[1, i],
        range(x, 9.99, length = 200),
        axis = (
            yscale = log10,
            yticks = LogTicks(IntegerTicks()), # the LogTicks wrapper takes care of the log transform before finding the IntegerTicks
            ytickformat = xs -> string.(xs), # this should usually format the resulting values as normal decimal numbers without trailing zeros 
            yminorgridvisible = true,
            yminorticks = IntervalsBetween(10),
            yminorticksvisible = true,
        )
    )
end

f

```

 ![grafik](https://canada1.discourse-cdn.com/flex030/uploads/pumas/original/1X/c8bb2801020539dea4c3f475e7ab4c59040c93d4.png)

---

<div class="post-metadata">

**Author:** ![bobbrown](https://avatars.discourse-cdn.com/v4/letter/b/c2a13f/32.png) [@bobbrown](https://discourse.pumas.ai/u/bobbrown)\
**Post date:** [February 24, 2022, 3:19pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/22 "2022-02-24T15:19:15Z")

</div>

Thank you very much @vijay @storopoli I was able to generate a quality graph finally using your code. I am touched by the help I am receiving. I was also able to control the marker, line sizes, marker color. The only thing I could not successfully change was the linecolor (see code below). Markercolor works, but not linecolor, not sure why.

```auto
ot = observations_vs_time(pop_nca, 
                                axis = (xlabel = "Time (hours)", 
                                        ylabel = "Concentration (μg/mL)",
                                        yscale=log10, ytickformat=x -> string.(round.(x; digits=1)), 
                                        yticks = [0.1, 1, 10],
                                        ygridwidth = 3, 
                                        yminorticksvisible = true,
                                        yminorgridvisible = true,
                                        yminorticks = IntervalsBetween(10),
                                        xminorticksvisible = true,
                                        xminorgridvisible = true,
                                        xminorticks = IntervalsBetween(5),
                                        limits = (nothing, nothing, nothing, 20),
                                        spinewidth = 2),
                                        columns = 4, rows = 3,
                                        markersize = 8,
                                        markercolor = :green,
                                        linewidth = 2,
                                        linecolor = :black,
                                        facet = ( combinelabels = true,))
#
save("../code/practice/nibr/data/linear_pk_plots.pdf", ot)

```

 ![image](https://canada1.discourse-cdn.com/flex030/uploads/pumas/original/1X/22f0e9f4bf0494203357bea1f2482848618660ae.jpeg)

---

<div class="post-metadata">

**Author:** ![bobbrown](https://avatars.discourse-cdn.com/v4/letter/b/c2a13f/32.png) [@bobbrown](https://discourse.pumas.ai/u/bobbrown)\
**Post date:** [February 24, 2022, 3:25pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/23 "2022-02-24T15:25:38Z")

</div>

@Michael Thank you. That was it. paginate = true was the culprit. The code that @vijay @storopoli provided did allow me to control the cosmetics; however it only produces graphs for the first 12 subjects (perhaps due to the columns=4, rows=3). There are a total of 50 subjects. If I increase columns/rows, the plots are squished. I am unsure as to first generating all 50 profiles; and then save() them. Any advice?  
Bob

---

<div class="post-metadata">

**Author:** ![bobbrown](https://avatars.discourse-cdn.com/v4/letter/b/c2a13f/32.png) [@bobbrown](https://discourse.pumas.ai/u/bobbrown)\
**Post date:** [February 24, 2022, 3:29pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/24 "2022-02-24T15:29:43Z")

</div>

@julius Thank you. Unfortunately, I am unable to adapt the code to my data. My experience is more on the clinical side; and not on the software side. I barely manage. It’s my bad. The for loop etc is where I am lost, as to its application to my data. The code provided @vijay @storopoli seem to do the job, unless your code is more efficient.  
Bob

---

<div class="post-metadata">

**Author:** ![Michael](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.pumas.ai/michael/32/818_2.png) [@Michael](https://discourse.pumas.ai/u/Michael)\
**Post date:** [February 24, 2022, 3:30pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/25 "2022-02-24T15:30:30Z")

</div>

The `Vector{Figure}` that `paginate = true` generates could be saved out to individual numbered PDFs using something like the following:

```julia
foreach(enumerate(pk_plots)) do (nth, plot)
    save("plot-$nth.pdf", plot)
end

```

---

<div class="post-metadata">

**Author:** ![julius](https://avatars.discourse-cdn.com/v4/letter/j/ecd19e/32.png) [@julius](https://discourse.pumas.ai/u/julius)\
**Post date:** [February 24, 2022, 3:41pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/26 "2022-02-24T15:41:50Z")

</div>

Sorry for confusing you, the for loop was not related to your data but should just show how the tick finding works with three different y limits. The solution you were given before is fine if you know the y tickpositions beforehand. My solution is automatic, so it could also be useful. You only need this part

```julia
struct IntegerTicks end
MakieLayout.get_tickvalues(::IntegerTicks, vmin, vmax) = ceil(Int, vmin) : floor(Int, vmax)

```

And then pass the `yticks` and `ytickformat` keyword arguments as shown

```julia
        axis = (
            yscale = log10,
            yticks = LogTicks(IntegerTicks()), # the LogTicks wrapper takes care of the log transform before finding the IntegerTicks
            ytickformat = xs -> string.(xs), # this should usually format the resulting values as normal decimal numbers without trailing zeros 

```

---

<div class="post-metadata">

**Author:** ![bobbrown](https://avatars.discourse-cdn.com/v4/letter/b/c2a13f/32.png) [@bobbrown](https://discourse.pumas.ai/u/bobbrown)\
**Post date:** [February 24, 2022, 4:02pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/27 "2022-02-24T16:02:17Z")

</div>

Aha! @Michael Thank you. I guess there is no equivalent of knitr so all graphs are in one file. Imagine 5 PDFs for every type of graph one produces. Any way to consolidate?  
Bob

---

<div class="post-metadata">

**Author:** ![Michael](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.pumas.ai/michael/32/818_2.png) [@Michael](https://discourse.pumas.ai/u/Michael)\
**Post date:** [February 24, 2022, 4:07pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/28 "2022-02-24T16:07:34Z")

</div>

`report(pk_plots; title = "my title")` might be what you’re wanting in that case, which should generate a single PDF document with all the paginated plots.

---

<div class="post-metadata">

**Author:** ![bobbrown](https://avatars.discourse-cdn.com/v4/letter/b/c2a13f/32.png) [@bobbrown](https://discourse.pumas.ai/u/bobbrown)\
**Post date:** [February 24, 2022, 4:10pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/29 "2022-02-24T16:10:18Z")

</div>

Wow that would be great. How do I embed my graph with my specifications into this report?

---

<div class="post-metadata">

**Author:** ![Michael](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.pumas.ai/michael/32/818_2.png) [@Michael](https://discourse.pumas.ai/u/Michael)\
**Post date:** [February 24, 2022, 4:15pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/30 "2022-02-24T16:15:12Z")

</div>

> [@bobbrown](#):
>
> How do I embed my graph with my specifications into this report?

Could you describe in more detail what you would like to embed in the generated PDF? Currently `report` has limited customization options, we will be expanding on it in future releases though.

---

<div class="post-metadata">

**Author:** ![bobbrown](https://avatars.discourse-cdn.com/v4/letter/b/c2a13f/32.png) [@bobbrown](https://discourse.pumas.ai/u/bobbrown)\
**Post date:** [February 24, 2022, 4:16pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/31 "2022-02-24T16:16:43Z")

</div>

@Michael sure. I would like to retain the plot attributes as below in the report. Can this done?

```auto
ot = observations_vs_time(pop_nca, 
                                axis = (xlabel = "Time (hours)", 
                                        ylabel = "Concentration (μg/mL)",
                                        yscale=log10, ytickformat=x -> string.(round.(x; digits=1)), 
                                        yticks = [0.1, 1, 10],
                                        ygridwidth = 3, 
                                        yminorticksvisible = true,
                                        yminorgridvisible = true,
                                        yminorticks = IntervalsBetween(10),
                                        xminorticksvisible = true,
                                        xminorgridvisible = true,
                                        xminorticks = IntervalsBetween(5),
                                        limits = (nothing, nothing, nothing, 20),
                                        spinewidth = 2),
                                        columns = 4, rows = 3,
                                        markersize = 8,
                                        markercolor = :green,
                                        linewidth = 2,
                                        linecolor = :black,
                                        facet = ( combinelabels = true,))

```

---

<div class="post-metadata">

**Author:** ![Michael](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.pumas.ai/michael/32/818_2.png) [@Michael](https://discourse.pumas.ai/u/Michael)\
**Post date:** [February 24, 2022, 4:19pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/32 "2022-02-24T16:19:34Z")

</div>

That should work fine. `report` uses the same output as `save(..., ot)` so anything that appears when you manually call `save` on a `Figure` should also appear in the PDF generated by `report`.

---

<div class="post-metadata">

**Author:** ![bobbrown](https://avatars.discourse-cdn.com/v4/letter/b/c2a13f/32.png) [@bobbrown](https://discourse.pumas.ai/u/bobbrown)\
**Post date:** [February 24, 2022, 4:28pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/33 "2022-02-24T16:28:35Z")

</div>

@Michael may be I am not communicating clearly here. I have 50 profiles, which have to spread out on multiple pages. Let us say 4 columns x 3 rows x 5 pages. Here is the code based on your advice I used:

```auto
#
pk_log_plots = observations_vs_time(pop_nca, 
                                axis = (xlabel = "Time (hours)", 
                                        ylabel = "Concentration (μg/mL)",
                                        yscale=log10, ytickformat=x -> string.(round.(x; digits=1)), 
                                        yticks = [0.1, 1, 10],
                                        ygridwidth = 3, 
                                        yminorticksvisible = true,
                                        yminorgridvisible = true,
                                        yminorticks = IntervalsBetween(10),
                                        xminorticksvisible = true,
                                        xminorgridvisible = true,
                                        xminorticks = IntervalsBetween(5),
                                        limits = (nothing, nothing, nothing, 20),
                                        spinewidth = 2),
                                        columns = 4, rows = 3,
                                        paginate = true,
                                        markersize = 8,
                                        markercolor = :green,
                                        linewidth = 2,
                                        linecolor = :black,
                                        facet = ( combinelabels = true,))
#
pk_log_plots[1]
pk_log_plots[2]
report(pk_log_plots; title = "pk_log_plots.PDF") 

```

The pk\_log\_plots.PDF contains only the first page. Please note I used: paginate=true. Hence I am able to view pk\_log\_plots[1], [2]…[6].

---

<div class="post-metadata">

**Author:** ![vijay](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.pumas.ai/vijay/32/96_2.png) [@vijay](https://discourse.pumas.ai/u/vijay)\
**Post date:** [February 24, 2022, 4:35pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/34 "2022-02-24T16:35:40Z")

</div>

hi @bobbrown  
I need to check if this works in your version on [juliahub.com](http://juliahub.com) but please try this

```julia
report(pk_log_plots, 
      title = "Individual fits", 
      output = "./foldertosaveplots",
      header = "Single Ascending Dose",
      footer = "Confidential")

```

check for the pdf in the working directory

---

<div class="post-metadata">

**Author:** ![Michael](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.pumas.ai/michael/32/818_2.png) [@Michael](https://discourse.pumas.ai/u/Michael)\
**Post date:** [February 24, 2022, 4:40pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/35 "2022-02-24T16:40:12Z")

</div>

As @vijay mentions above, `output = "..."` can be used to set where the report PDF appears, it defaults to a `output` folder in the current working directory. Is there anything in that folder (if it exists)?

---

<div class="post-metadata">

**Author:** ![bobbrown](https://avatars.discourse-cdn.com/v4/letter/b/c2a13f/32.png) [@bobbrown](https://discourse.pumas.ai/u/bobbrown)\
**Post date:** [February 24, 2022, 5:24pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/36 "2022-02-24T17:24:09Z")

</div>

@Michael @vijay We have a winner finally! I was able to output all the plots into this PDF file. Thank you all.

 ![image](https://canada1.discourse-cdn.com/flex030/uploads/pumas/original/1X/849e57aab99f5ea6895aacfafcfa177dd8081399.png)

Now I am getting greedy (and have nothing else to do). I also have another plot for average PK profiles: avg\_pk\_plots. I tried if I can concatenate the two sets of plots using this code. Of course, it did not work.

```auto
report([pk_log_plots; avg_pk_plots],
     #(pk_log_plots; avg_pk_plots)
     #(pk_log_plots, avg_pk_plots) 
      title = "Individual Semi-Log Exploratory Plots", 
      output = "./practice/nibr/data/plots",
      header = "Single Ascending Dose",
      footer = "Confidential")

```

I do want to do a pulse-check. Hope these discussions are useful for other users as well. You both seem to be pros. I am happy share my entire project work here, so others can learn as well. Not imposing anything. Just a thought.  
Bob

---

<div class="post-metadata">

**Author:** ![bobbrown](https://avatars.discourse-cdn.com/v4/letter/b/c2a13f/32.png) [@bobbrown](https://discourse.pumas.ai/u/bobbrown)\
**Post date:** [February 24, 2022, 5:37pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/37 "2022-02-24T17:37:52Z")

</div>

@storopoli your code was immensely helpful. I still could not get linecolor = :red to work. Anything that you could see in my code that is erroneous?  
B

---

<div class="post-metadata">

**Author:** ![Michael](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.pumas.ai/michael/32/818_2.png) [@Michael](https://discourse.pumas.ai/u/Michael)\
**Post date:** [February 24, 2022, 5:43pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/38 "2022-02-24T17:43:55Z")

</div>

It’ll be `color = :red` rather than `linecolor = :red` for `observations_vs_time` if I recall correctly.

---

<div class="post-metadata">

**Author:** ![bobbrown](https://avatars.discourse-cdn.com/v4/letter/b/c2a13f/32.png) [@bobbrown](https://discourse.pumas.ai/u/bobbrown)\
**Post date:** [February 24, 2022, 5:48pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/39 "2022-02-24T17:48:35Z")

</div>

That worked. I could not have a guessed it, given there is a markercolor argument. Thank you.

---

<div class="post-metadata">

**Author:** ![vijay](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.pumas.ai/vijay/32/96_2.png) [@vijay](https://discourse.pumas.ai/u/vijay)\
**Post date:** [February 24, 2022, 6:26pm UTC](https://discourse.pumas.ai/t/nibr-data-analysis/630/40 "2022-02-24T18:26:40Z")

</div>

> [@bobbrown](#):
>
> Now I am getting greedy (and have nothing else to do). I also have another plot for average PK profiles: avg\_pk\_plots. I tried if I can concatenate the two sets of plots using this code. Of course, it did not work.

@bobbrown you need to do this

```julia
report(vcat(pk_log_plots, avg_pk_plots),
      title = "Summary and Individual Semi-Log Exploratory Plots", 
      output = "./practice/nibr/data/plots",
      header = "Single Ascending Dose",
      footer = "Confidential")

```

some other julia experts can weigh in here, but the pattern of concatenating two vectors in julia is that you need to split the vectors into individual elements using `...` and then put them together. See the example below.

```julia
julia> a = [1,2,3]
3-element Vector{Int64}:
 1
 2
 3

julia> b = [4, 5, 6]
3-element Vector{Int64}:
 4
 5
 6

julia> [a, b]
2-element Vector{Vector{Int64}}:
 [1, 2, 3]
 [4, 5, 6]

julia> [a..., b...]
6-element Vector{Int64}:
 1
 2
 3
 4
 5
 6

#UPDATE: Based on Michael's response below
julia> vcat(a, b)
6-element Vector{Int64}:
 1
 2
 3
 4
 5
 6

```

The `report` function only takes a vector of plots and not a `vector` of `vectors`.

> [@bobbrown](#):
>
> I do want to do a pulse-check. Hope these discussions are useful for other users as well. You both seem to be pros.

We are happy to have these discussions, Please keep them coming!

> [@bobbrown](#):
>
> I am happy share my entire project work here, so others can learn as well. Not imposing anything. Just a thought.

That would be awesome, please share your experiences. In the meanwhile, for those reading the thread, I summarized all the code required till now below.

```julia
using Pumas
using PumasUtilities
using Dates
using CairoMakie
using AlgebraOfGraphics
using DataFramesMeta
df = CSV.read("Single_Ascending_Dose_Dataset2.csv", DataFrame, missingstrings = ["NA"])
df = @rsubset df :TIME >= 0
@rtransform! df route = "ev"
## map NCA data from CSV
ncapop = read_nca(df,
                id = :ID, time = :NOMTIME, amt = :AMT, route = :route,
                observations = :LIDV, 
                group = [:DOSE])

#plot means               
avg_pk_plots = summary_observations_vs_time(ncapop, 
                                  color = :black, linewidth = 2, whiskerwidth = 8,
                                  paginate = true,
                                  limit = 1,
                                  axis = (xlabel = "Time (hours)", 
                                            ylabel = "Concentration (μg/mL)",
                                            yscale=log10, ytickformat=x -> string.(round.(x; digits=1)), 
                                            yticks = [0.1, 1, 10],
                                            ygridwidth = 3, 
                                            yminorgridcolor = :darkgrey,
                                            yminorticksvisible = true,
                                            yminorgridvisible = true,
                                            yminorticks = IntervalsBetween(10),
                                            xminorticksvisible = true,
                                            xminorgridvisible = true,
                                            xminorticks = IntervalsBetween(5),
                                            limits = (nothing, nothing, nothing, 30),
                                            spinewidth = 2),
                                    #facet = ( combinelabels = true,),
                                    figure = (resolution = (800,800),
                                                        fontsize = 22),)
                                  
pk_log_plots = observations_vs_time(ncapop, paginate = true, color = :black,
                                axis = (xlabel = "Time (hours)", 
                                        ylabel = "Concentration (μg/mL)",
                                        yscale=log10, ytickformat=x -> string.(round.(x; digits=1)), 
                                        yticks = [0.1, 1, 10],
                                        ygridwidth = 3, 
                                        yminorticksvisible = true,
                                        yminorgridvisible = true,
                                        yminorticks = IntervalsBetween(10),
                                        xminorticksvisible = true,
                                        xminorgridvisible = true,
                                        xminorticks = IntervalsBetween(5),
                                        limits = (nothing, nothing, nothing, 20),
                                        spinewidth = 2),
                                        columns = 4, rows = 4,
                                        facet = ( combinelabels = true,))

report([pk_log_plots..., avg_pk_plots...],
      title = "Summary and Individual Semi-Log Exploratory Plots", 
      output = "./practice/nibr/data/plots",
      header = "Single Ascending Dose",
      footer = "Confidential")

```

Hope this helps!

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