ggfortify | Define fortify and autoplot functions | Data Visualization library

by sinhrks R Version: v0.4.15 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | ggfortify Summary

ggfortify is a R library typically used in Analytics, Data Visualization applications. ggfortify has no bugs, it has no vulnerabilities and it has low support. However ggfortify has a Non-SPDX License. You can download it from GitHub.

Define fortify and autoplot functions to allow ggplot2 to handle some popular R packages.

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ggfortify has a low active ecosystem.

It has 511 star(s) with 64 fork(s). There are 23 watchers for this library.

It had no major release in the last 12 months.

There are 19 open issues and 70 have been closed. On average issues are closed in 84 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of ggfortify is v0.4.15

Quality

ggfortify has 0 bugs and 0 code smells.

Security

ggfortify has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

ggfortify code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

ggfortify has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

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ggfortify releases are available to install and integrate.

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ggfortify Examples and Code Snippets

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Community Discussions

Trending Discussions on ggfortify

Why doesn't this survfit plot start at 100%

Survival analysis in R; creating interactive kaplan-meier plot in with plotly package

Difference ggplot2 and autoplot() after prcomp?

Draw only 2 ellipses in PCA plot (instead of 20)

Error adding new curve to survival curve in ggplot?

attributes in autoplot() function do not do anything , R

Removing the inner color of the ellipse in PCA

How to overlapping the different information in the PCA plot?

How to edit legend in ggfortify in R

2 survival functions, 1 left-truncated, 1 not truncated. How create survival function in R that assumes same experience over the truncated interval?

QUESTION

Why doesn't this survfit plot start at 100%

Asked 2022-Mar-31 at 07:04

When I plot the survfit plot of data with two different censoring events, the overall plot (s0) doesnt start at time = 0, pstate = 100%, but jumps to 100% when the first cencoring event occurs.

Here you can see in an example, where the jump occurs at time 1, that is the first cencoring event.

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ANSWER

Answered 2022-Mar-30 at 22:53

This does seem to be a bug in ggfortify. As a temporary fix, you can set the survival percentage at t = 0 to 100% by doing:

Source https://stackoverflow.com/questions/71679656

QUESTION

Survival analysis in R; creating interactive kaplan-meier plot in with plotly package

Asked 2022-Feb-22 at 13:01

I am generating kaplan-meier plots within R and I was wondering if there were a way to create an interactive kaplan-meier plot using the plotly package? Ideally, I would like to be able to trace the survival "line" using my mouse cursor with the plotly tooltip box telling me the group, the survival rate, and the time as well.

Here is an mock example of survival analysis that I would like to recreate within plotly:-

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ANSWER

Answered 2022-Feb-22 at 13:01

One option is to extract the ggplot figure from a ggsurvplot object.

Source https://stackoverflow.com/questions/71220061

QUESTION

Difference ggplot2 and autoplot() after prcomp?

Asked 2022-Feb-22 at 12:44

I made a PCA plot with autoplot(), but I wanted to have ellipses around only 2 of the groups instead of all 3. Therefore I switched to ggplot. However, it seems that my axes are different between autoplot and ggplot methods. Look at the difference between p1 and p2:

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ANSWER

Answered 2022-Feb-22 at 12:44

In the autoplot method, the principal components are scaled, so to get the same result you would do:

Source https://stackoverflow.com/questions/71221048

QUESTION

Draw only 2 ellipses in PCA plot (instead of 20)

Asked 2022-Feb-22 at 12:07

I have a PCA plot created with ggplot/ggfortify and the function autoplot(), such as in this question: Change point colors and color of frame/ellipse around points

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ANSWER

Answered 2022-Feb-21 at 21:44

The problem with using autoplot is that, although it is great for producing nice visualizations of common data structures and models with little effort, it doesn't give you the full freedom to customize the plot. However, it is pretty straightforward to do the whole thing within ggplot. The following is a full reprex:

Source https://stackoverflow.com/questions/71212997

QUESTION

Error adding new curve to survival curve in ggplot?

Asked 2022-Feb-21 at 04:16

I want to add a new line and confidence band to a survival analysis plot (Kaplan-Meier curve) created using autoplot from the ggfortify package.

However, I receive an error when using geom_ribbon but not when using geom_line. The minimal example below illustrates the issue.

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ANSWER

Answered 2022-Feb-21 at 04:16

If you specify inherit.aes = FALSE in geom_ribbon() you avoid that specific error, i.e.

Source https://stackoverflow.com/questions/71199927

QUESTION

attributes in autoplot() function do not do anything , R

Asked 2022-Feb-11 at 22:10

I have a dataset with time, status ( 1=death, 0 = censored), treatement =1,2 .
I create my survival object km_2, I want to plot Kaplan-Meijer plot using autoplot(). I do not know what my mistake is but setting the attributes ( legendLabs for example ) do not make any change to the basic KM plot.

...

ANSWER

Answered 2022-Feb-11 at 22:10

There are a few things to point out here. Firstly, autoplot is a generic function, so the method used and the arguments it accepts depends on the type of object you are passing to it. In this case, you are passing a survfit object, and you will be able to see the correct parameters to use if you type ?autoplot.survfit into the console.

From this you will see that there is no legendLabs or plotTable option, and that the alpha for the confidence intervals is controlled with conf.int.alpha = . Similarly, the censoring shape is controlled with censor.shape.

Another issue is that there doesn't seem to be a way to change the factor labels in the legend, but in this case it is easy enough to change them in the data when you create the survfit object.

Lastly, it's a good idea to make a reproducible example if you want prompt and useful answers. It took a while to recreate a reasonable data structure to test and demonstrate this answer.

Source https://stackoverflow.com/questions/71086121

QUESTION

Removing the inner color of the ellipse in PCA

Asked 2021-Dec-14 at 02:35

Does anyone know how to change the transparency(or alpha) of the color in the ellipse?
I want to remain only the line of boundary in the plot.
I tried to mimic the code in this site: http://www.sthda.com/english/wiki/fviz-pca-quick-principal-component-analysis-data-visualization-r-software-and-data-mining

But I could not find the option about the alpha value of the ellipse color.

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ANSWER

Answered 2021-Dec-14 at 02:35

You may use ellipse.alpha argument that can find here.

Source https://stackoverflow.com/questions/70343002

QUESTION

How to overlapping the different information in the PCA plot?

Asked 2021-Nov-01 at 13:42

I tried to draw the modified PCA plot representing two types of categories.
For example, I want to draw PCA with 1) PCA ellipse based on Kingdom, 2) PCA sample points colored with Class variable.
Here is the example dataset.

...

ANSWER

Answered 2021-Nov-01 at 13:42

You can specify the frame.colour for the ellipses and the colour for the points:

Source https://stackoverflow.com/questions/69797480

QUESTION

How to edit legend in ggfortify in R

Asked 2021-Oct-20 at 00:58

I am using carData::Rossi data to estimate a survival curve. This is the code I used to generate the plot:

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ANSWER

Answered 2021-Oct-19 at 01:38

Instead of strata = "Raza", you using both color = "Raza" and fill = "Raza" will works.

Source https://stackoverflow.com/questions/69623966

QUESTION

2 survival functions, 1 left-truncated, 1 not truncated. How create survival function in R that assumes same experience over the truncated interval?

Asked 2021-Sep-13 at 19:09

I have two survival functions, one is not truncated so I have experience for all time periods. The other is left-truncated until t = 4, so it has no experience until t > 4. I can plot the two together in the following code in R using the survival package.

...

ANSWER

Answered 2021-Sep-13 at 19:09

If you look at the structure of the survival_fn object (which is not a function but rather a list), you see:

Source https://stackoverflow.com/questions/69094265

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