adding-plotBuilder #345

bmatyasb · 2025-01-29T20:10:12Z

No description provided.

FBartos · 2025-01-30T08:11:45Z

The PR above fixes the wrapper issues. You should be able to load the module and get the main analysis function running.
(you now get errors about undefined '%>%' command)

FBartos · 2025-01-30T08:28:38Z

The code is nicely formated and quite readable, I think it's pretty much compliant with the JASP style. Very nice! There are two issue I will need you to help us with (which is also what Don mentioned in the Mattermost channel). That's:

not importing the complete package namespaces, i.e., your original NAMESPACE file had,

import(jaspBase)
import(jaspGraphs)
import(ggplot2)
import(tidyplots)
import(rlang)
import(dplyr)
import(tidyr)
import(ggprism)
import(patchwork)
import(tidyverse)
import(ggpubr)
import(ggeasy)
import(forcats)

but this easily messes the internal JASP namespace. Instead, it's highly preferred to use e.g.,
ggplot2::ggplot() + ggplot2::theme_void() notation

trimming down on some of the large package dependencies wherever possible. The main issues are

tidyverse
tidyplots
tidyr
dplyr
(am I missing some @vandenman ?). We cannot really ship those packages because a) they have an extremely large dependency base and the potential of breaking JASP during the update is too big, and b) they are most wrappers meant for analysis scripts but not for package development - they are not very stable and they might change (which would brick the analysis). Maybe Don has a more precise explanation on this.

This will, unfortunately, require some rewriting of the code, but pretty much tidyverse convenience functions have baseR alternatives. I don't really use tidyverse at all so it's a bit challenging to me figure out what are all the imported functions (apart from the pipe signs haha), but I would guess that using ChatGPT like tool could make this not too difficult. Does this seem reasonable to you and that it would be manageable for you to implement?

bmatyasb · 2025-01-30T08:36:03Z

trying to weed out tidyverse, tidyr and dplyr. Obviously tidyplot will stay, because it would be more complicated in ggplot. i will try, but i can't promise to succeed :D but i will let you know in time if i can't do it.

…

On Thu, 30 Jan 2025 at 09:29, František Bartoš ***@***.***> wrote: The code is nicely formated and quite readable, I think it's pretty much compliant with the JASP style. Very nice! There are two issue I will need you to help us with (which is also what Don mentioned in the Mattermost channel). That's: 1. *not importing the complete package namespaces*, i.e., your original NAMESPACE file had, import(jaspBase) import(jaspGraphs) import(ggplot2) import(tidyplots) import(rlang) import(dplyr) import(tidyr) import(ggprism) import(patchwork) import(tidyverse) import(ggpubr) import(ggeasy) import(forcats) but this easily messes the internal JASP namespace. Instead, it's highly preferred to use e.g., ggplot2::ggplot() + ggplot2::theme_void() notation 2. *trimming down on some of the large package dependencies wherever possible*. The main issues are - tidyverse - tidyplots - tidyr - dplyr (am I missing some @vandenman <https://github.com/vandenman> ?). We cannot really ship those packages because a) they have an extremely large dependency base and the potential of breaking JASP during the update is too big, and b) they are most wrappers meant for analysis scripts but not for package development - they are not very stable and they might change (which would brick the analysis). Maybe Don has a more precise explanation on this. This will, unfortunately, require some rewriting of the code, but pretty much tidyverse convenience functions have baseR alternatives. I don't really use tidyverse at all so it's a bit challenging to me figure out what are all the imported functions (apart from the pipe signs haha), but I would guess that using ChatGPT like tool could make this not too difficult. Does this seem reasonable to you and that it would be manageable for you to implement? — Reply to this email directly, view it on GitHub <#345 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AVW2D7J2ZJKHSNDCEHYKGUD2NHPE3AVCNFSM6AAAAABWDWDJA6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMRTHAZTIOBZGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

FBartos · 2025-01-30T08:50:19Z

tidyr and dplyr are both imported by tidyplots (so removing them while keeping tidyplots won't help that much). I think tidyverse has to go for sure, but @vandenman will have the final say for the rest

EJWagenmakers · 2025-01-30T08:55:59Z

As an aside, I have asked @PabRod to stress this point in the documentation. If we make a list of things that contributors ought to be aware of, this one might break into the top 3....

bmatyasb · 2025-01-30T08:56:35Z

OK, I look forward to your reply. unfortunately, i am not able to replace tidyplot. the module has become possible because tidyplot makes the implementation of ggplot quite easy :(... but i think i can solve the tidyvers.

…

On Thu, 30 Jan 2025 at 09:50, František Bartoš ***@***.***> wrote: tidyr and dplyr are both imported by tidyplots (so removing them while keeping tidyplots won't help that much). I think tidyverse has to go for sure, but @vandenman <https://github.com/vandenman> will have the final say for the rest — Reply to this email directly, view it on GitHub <#345 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AVW2D7IVOEQMAN6NGYIXJU32NHRWFAVCNFSM6AAAAABWDWDJA6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMRTHA3TIMZXGE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

EJWagenmakers · 2025-01-30T08:59:29Z

Also, will this still be as relevant when we have our online module library in llace? I know this will take a while to get done, but still useful to know [correction: we want this in Des riptives, so part of the JASP core functionality]

vandenman · 2025-01-30T09:48:20Z

Going by the list here I would suggest

package	keep
ggplot2	👍
tidyplots	👍
rlang	👍
dplyr	👍
tidyr	👍
forcats	👍
patchwork	👍
ggprism	❌
tidyverse	❌
ggeasy	❌
ggpubr	❓

ggpubr is a bit of a questionable case, because since both jaspGraphs and tidyplots use it it is reeled in anyway. But in general, try to keep the dependencies as lean as possible. So don't use tidyverse directly but figure out what subpackage you need from it. Likewise, we prefer not to reel in things like ggeasy and instead do the theming manually. Regarding ggprism, it's tricky to figure out where you use it at the moment (due to import instead of importFrom in the namespace) but if it's about the color schemes then we typically add these in jaspGraphs.

A good rule of thumb with dependencies (that we sadly aren't very strict about) is that everything in github.com/tidyverse and github.com/r-lib is fine to use, and the rest we look at on a case-by-case basis.

vandenman · 2025-01-30T09:49:14Z

also, you need to adjust the DESCRIPTION file otherwise the unit tests will surely fail to install the package.

bmatyasb · 2025-01-30T10:11:10Z

ggprism this should definitely go? i don't know how else i can easily solve the problem of adding p values to the plots.

…

On Thu, 30 Jan 2025 at 10:49, Don van den Bergh ***@***.***> wrote: also, you need to adjust the DESCRIPTION file otherwise the unit tests will surely fail to install the package. — Reply to this email directly, view it on GitHub <#345 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AVW2D7OGV2OIDZIXRCL2NGT2NHYTBAVCNFSM6AAAAABWDWDJA6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMRUGAYDKMRQHA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

vandenman · 2025-01-30T10:24:01Z

what about ggpubr::geom_bracket? that looks quite similar to ggprism::add_pvalue.

bmatyasb · 2025-01-30T10:27:04Z

okay, i try to solve it with ggpubr! thanks.

…

On Thu, 30 Jan 2025 at 11:24, Don van den Bergh ***@***.***> wrote: what about ggpubr::geom_bracket <https://rpkgs.datanovia.com/ggpubr/reference/geom_bracket.html>? that looks quite similar to ggprism::add_pvalue <https://csdaw.github.io/ggprism/reference/add_pvalue.html>. — Reply to this email directly, view it on GitHub <#345 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AVW2D7PBLU3FHK3BQZBDF2L2NH4VRAVCNFSM6AAAAABWDWDJA6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMRUGA4DKOJWG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

bmatyasb · 2025-01-30T16:52:29Z

Am I allowed to use import() or importFrom(), or library() inside the script, or should I use the package::function format? Mátyás Bukva ***@***.***> ezt írta (időpont: 2025. jan. 30., Cs 11:26):

…

okay, i try to solve it with ggpubr! thanks. On Thu, 30 Jan 2025 at 11:24, Don van den Bergh ***@***.***> wrote: > what about ggpubr::geom_bracket > <https://rpkgs.datanovia.com/ggpubr/reference/geom_bracket.html>? that > looks quite similar to ggprism::add_pvalue > <https://csdaw.github.io/ggprism/reference/add_pvalue.html>. > > — > Reply to this email directly, view it on GitHub > <#345 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AVW2D7PBLU3FHK3BQZBDF2L2NH4VRAVCNFSM6AAAAABWDWDJA6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMRUGA4DKOJWG4> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> >

bmatyasb · 2025-01-30T16:55:02Z

Sorry, import without brackets of course :D Mátyás Bukva ***@***.***> ezt írta (időpont: 2025. jan. 30., Cs 17:52):

…

Am I allowed to use import() or importFrom(), or library() inside the script, or should I use the package::function format? Mátyás Bukva ***@***.***> ezt írta (időpont: 2025. jan. 30., Cs 11:26): > okay, i try to solve it with ggpubr! thanks. > > On Thu, 30 Jan 2025 at 11:24, Don van den Bergh ***@***.***> > wrote: > >> what about ggpubr::geom_bracket >> <https://rpkgs.datanovia.com/ggpubr/reference/geom_bracket.html>? that >> looks quite similar to ggprism::add_pvalue >> <https://csdaw.github.io/ggprism/reference/add_pvalue.html>. >> >> — >> Reply to this email directly, view it on GitHub >> <#345 (comment)>, >> or unsubscribe >> <https://github.com/notifications/unsubscribe-auth/AVW2D7PBLU3FHK3BQZBDF2L2NH4VRAVCNFSM6AAAAABWDWDJA6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMRUGA4DKOJWG4> >> . >> You are receiving this because you authored the thread.Message ID: >> ***@***.***> >> >

bmatyasb · 2025-01-30T17:58:49Z

nothing, I solved what I asked for

…

On Thu, 30 Jan 2025 at 17:54, Mátyás Bukva ***@***.***> wrote: Sorry, import without brackets of course :D Mátyás Bukva ***@***.***> ezt írta (időpont: 2025. jan. 30., Cs 17:52): > Am I allowed to use import() or importFrom(), or library() inside the > script, or should I use the package::function format? > > Mátyás Bukva ***@***.***> ezt írta (időpont: 2025. jan. 30., > Cs 11:26): > >> okay, i try to solve it with ggpubr! thanks. >> >> On Thu, 30 Jan 2025 at 11:24, Don van den Bergh < >> ***@***.***> wrote: >> >>> what about ggpubr::geom_bracket >>> <https://rpkgs.datanovia.com/ggpubr/reference/geom_bracket.html>? that >>> looks quite similar to ggprism::add_pvalue >>> <https://csdaw.github.io/ggprism/reference/add_pvalue.html>. >>> >>> — >>> Reply to this email directly, view it on GitHub >>> <#345 (comment)>, >>> or unsubscribe >>> <https://github.com/notifications/unsubscribe-auth/AVW2D7PBLU3FHK3BQZBDF2L2NH4VRAVCNFSM6AAAAABWDWDJA6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMRUGA4DKOJWG4> >>> . >>> You are receiving this because you authored the thread.Message ID: >>> ***@***.***> >>> >>

FBartos · 2025-01-31T07:50:27Z

I think library(package) should never be done because it loads the whole package namespace into the current package (which can create a lot of mess).

When JASP loads a module, it loads the namespace of all its analyses (in the same way as if you develop an R package). It is very easy to get namespace conflicts among analyses within the same module. Therefore, the package::function format is almost always preferred as it ascertains that the correct function is called (even when multiple packages export the same function) and the overall module namespace remains concise.

vandenman · 2025-01-31T12:42:41Z

Am I allowed to use import() or importFrom(), or library() inside the
script, or should I use the package::function format?

never library, import is fine for e.g., jaspBase. importFrom I'd use if you use have a function from a package that you use often. pkg::function I'd use in most other cases.

bmatyasb · 2025-02-03T12:33:45Z

hi! today I finished what you asked me to do. so, what's left: ggplot2 tidyplots rlang dplyr tidyr forcats patchwork ggpubr ggpubr was also left as discussed because of the p value. package::function() "annotation" was used everywhere (except for the base R functions). I fixed the qml code in one or two lines, and I also touched the R script in a few places. the changes are committed

…

On Fri, 31 Jan 2025 at 13:43, Don van den Bergh ***@***.***> wrote: Am I allowed to use import() or importFrom(), or library() inside the script, or should I use the package::function format? never library, import is fine for e.g., jaspBase. importFrom I'd use if you use have a function from a package that you use often. pkg::function I'd use in most other cases. — Reply to this email directly, view it on GitHub <#345 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AVW2D7JY3VWRBQE2NGXTDI32NNVVRAVCNFSM6AAAAABWDWDJA6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMRXGIYDGMRRHA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

bmatyasb · 2025-02-03T18:36:06Z

Sorry, the addition of the #2 tag was completely accidental

vandenman

Just went over the QML, see the comments below. Overall this looks really good and complete, thanks!

vandenman · 2025-02-04T09:29:48Z

inst/qml/jaspPlotBuilder.qml

+Form {
+    columns: 1
+
+    infoBottom:


Two things.

This looks generated. If it is, can you add the R code to generate this as a comment above this for future updates?

You can do string continuation with \ (see https://forum.qt.io/topic/113667/multiline-strings/2). Not sure how to handle \n though.

vandenman · 2025-02-04T09:30:12Z

inst/qml/jaspPlotBuilder.qml

+    /// Here begins the main plot control
+    ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+
+    TabView {


Could you please indent this with tabs instead of spaces? :)

inst/qml/jaspPlotBuilder.qml

vandenman · 2025-02-04T09:47:40Z

inst/qml/jaspPlotBuilder.qml

+                        DropDown {
+                            name: "sortYLabelsOrder"
+                            label: "Sort Y labels"
+                            values: ["Increasing", "Decreasing"]
+                            startValue: "Increasing"
+                        }
+
+                        DropDown {
+                            name: "aggregationFunY"
+                            label: "By"
+                            values: ["mean", "median"]
+                            startValue: "mean"
+                        }


qsTr for the labels and see other comment about values and startvalues.

vandenman · 2025-02-04T09:49:04Z

inst/qml/jaspPlotBuilder.qml

+                        DoubleField {
+                            name: "topMargin"
+                            label: "Top"
+                            value: 10
+                        }
+                        DoubleField {
+                            name: "bottomMargin"
+                            label: "Bottom"
+                            value: 10
+                        }
+                        DoubleField {
+                            name: "leftMargin"
+                            label: "Left"
+                            value: 10
+                        }
+                        DoubleField {
+                            name: "rightMargin"
+                            label: "Right"
+                            value: 10
+                        }


labels need qsTr.

vandenman · 2025-02-04T09:49:22Z

inst/qml/jaspPlotBuilder.qml

+                            { label: "Default: JASP colors", value: "colors_JASP" },
+                            { label: "Discrete: Friendly", value: "colors_discrete_friendly" },
+                            { label: "Discrete: Seaside", value: "colors_discrete_seaside" },
+                            { label: "Discrete: Apple", value: "colors_discrete_apple" },
+                            { label: "Discrete: Friendly Long", value: "colors_discrete_friendly_long" },
+                            { label: "Discrete: Okabe Ito", value: "colors_discrete_okabeito" },
+                            { label: "Discrete: IBM", value: "colors_discrete_ibm" },
+                            { label: "Discrete: Metro", value: "colors_discrete_metro" },
+                            { label: "Discrete: Candy", value: "colors_discrete_candy" },
+                            { label: "Discrete: Alger", value: "colors_discrete_alger" },
+                            { label: "Discrete: Rainbow", value: "colors_discrete_rainbow" },
+                            { label: "Continuous: Viridis", value: "colors_continuous_viridis" },
+                            { label: "Continuous: Magma", value: "colors_continuous_magma" },
+                            { label: "Continuous: Inferno", value: "colors_continuous_inferno" },
+                            { label: "Continuous: Plasma", value: "colors_continuous_plasma" },
+                            { label: "Continuous: Cividis", value: "colors_continuous_cividis" },
+                            { label: "Continuous: Rocket", value: "colors_continuous_rocket" },
+                            { label: "Continuous: Mako", value: "colors_continuous_mako" },
+                            { label: "Continuous: Turbo", value: "colors_continuous_turbo" },
+                            { label: "Continuous: Blue Pink Yellow", value: "colors_continuous_bluepinkyellow" },
+                            { label: "Diverging: Blue to Red", value: "colors_diverging_blue2red" },
+                            { label: "Diverging: Blue to Brown", value: "colors_diverging_blue2brown" },
+                            { label: "Diverging: BuRd", value: "colors_diverging_BuRd" },
+                            { label: "Diverging: BuYlRd", value: "colors_diverging_BuYlRd" },
+                            { label: "Diverging: Spectral", value: "colors_diverging_spectral" },
+                            { label: "Diverging: Icefire", value: "colors_diverging_icefire" }


labels need qsTr

inst/qml/jaspPlotBuilder.qml

shun2wang · 2025-02-04T10:29:35Z

R/jaspPlotBuilder.R

+  updatedPlots <- plotResults$updatedPlots
+
+  if (!is(jaspResults[["plotGridContainer"]], "JaspContainer")) {
+    plotGridContainer <- createJaspContainer(title = "Plot Grid")


plotGridContainer <- createJaspContainer(title = gettext("Plot Grid"))

we should mark this titles text by gettext/gettextf to make it translatable.

FBartos · 2025-02-04T10:31:07Z

inst/qml/jaspPlotBuilder.qml

+        name: "PlotBuilderTab"
+
+        rowComponent: Group {
+
+            childControlsArea.anchors.leftMargin: jaspTheme.contentMargin
+
+            Group{
+                columns:2
+                TextField {
+                    name: "plotId"
+                    label: qsTr("Plot ID")
+                    fieldWidth: 200
+                    placeholderText: qsTr("Enter Plot ID")
+                }
+


Suggested change

name: "PlotBuilderTab"

rowComponent: Group {

childControlsArea.anchors.leftMargin: jaspTheme.contentMargin

Group{

columns:2

TextField {

name: "plotId"

label: qsTr("Plot ID")

fieldWidth: 200

placeholderText: qsTr("Enter Plot ID")

}

name: "PlotBuilderTab"

newItemName: qsTr("Plot 1")

rowComponent: Group {

childControlsArea.anchors.leftMargin: jaspTheme.contentMargin

Group{

columns:2

Adding the newItemName automatically names the tabs "Plot 1", "Plot 2", ...

(and users can rename them by double clicking them)

These can be also used as the plotId - a bit of an annoying issue now is that you need to fill in the idea first, otherwise the whole analysis is terminated with an error. Using the tab names circumvents the issue (in case you names without spaces and special symbols, it should be easy to replace them with underscores using gsub etc?)

This needs to be propagated into the R-code. While now the code takes the plotId from options[["PlotBuilderTab"]][[1]][["plotId"]], now it should refer to the name in options[["PlotBuilderTab"]][[1]][["value"]]
(I did not do that as it's a too big change for a suggested change here)

that's a great idea! thanks a lot! just a couple of lines to rewrite and it works.

Thanks :) I will do a deeper dive and more suggestions once all the previous parts are addressed (it's a bit of a mess with al the qml suggestions right now) Could you maybe just prompt me to do so on mattermost?

Co-authored-by: Don van den Bergh <[email protected]>

inst/qml/jaspPlotBuilder.qml

Co-authored-by: Shun Wang <[email protected]>

and some commented script

namespace

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FBartos self-requested a review January 30, 2025 08:00

fix wrapper

51bfabd

FBartos requested a review from vandenman January 30, 2025 08:29

adding plot builder

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bmatyasb added 2 commits February 3, 2025 13:38

hotfix for proportion if RM true

e03f6e5

hotfix for proportion if RM true jasp-stats#2

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update description with imports

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Update inst/qml/jaspPlotBuilder.qml

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adding-plotBuilder #345

adding-plotBuilder #345

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adding-plotBuilder #345

Are you sure you want to change the base?

adding-plotBuilder #345

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