facets | implement Fraction and Copy number Estimate

 by   mskcc R Version: v0.6.2 License: No License

kandi X-RAY | facets Summary

kandi X-RAY | facets Summary

facets is a R library. facets has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

Algorithm to implement Fraction and Allele specific Copy number Estimate from Tumor/normal Sequencing. Travis CI (Linux & macOS) Test coverage. You can install the current version (along with the vignette) using the command. pctGCdata is a required package. So install that also (needs to be done only once). If you get an error message about pctGCdata use.
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              facets has a low active ecosystem.
              It has 116 star(s) with 58 fork(s). There are 75 watchers for this library.
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              It had no major release in the last 12 months.
              There are 113 open issues and 60 have been closed. On average issues are closed in 98 days. There are 2 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of facets is v0.6.2

            kandi-Quality Quality

              facets has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              facets does not have a standard license declared.
              Check the repository for any license declaration and review the terms closely.
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              Without a license, all rights are reserved, and you cannot use the library in your applications.

            kandi-Reuse Reuse

              facets releases are available to install and integrate.
              Installation instructions are not available. Examples and code snippets are available.

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            facets Key Features

            No Key Features are available at this moment for facets.

            facets Examples and Code Snippets

            No Code Snippets are available at this moment for facets.

            Community Discussions

            QUESTION

            Is there a way to find the names of the facets in a ggplot?
            Asked 2021-Jun-13 at 22:08

            I would like to add some curves to a ggplot with facets but I can not figure out how to correctly identify a particular panel with a particular name used for faceting. For instance:

            ...

            ANSWER

            Answered 2021-Jun-13 at 22:05

            We could extract the data.frame in layout

            Source https://stackoverflow.com/questions/67962978

            QUESTION

            how to create a wormplot (detrended Q-Q plot) in ggplot?
            Asked 2021-Jun-13 at 20:42

            Q-Q plot is a useful graphical device used to check for example normality of residuals. Q-Q plot is constructed by putting theoretical quantiles on x-axis and observed quantiles on the y-axis. In ggplot, this can be easily done using geom_qq and stat_qq. I would like to produce a wormplot, which is like a Q-Q plot, but on the y-axis, it has a difference between theoretical and observed quantiles (see the figure).

            Is there a way to do this in ggplot? For example, is there a simple way to change the y-axis of the geom_qq to show the difference between theoretical and observed quantiles? I know it should be possible to calculate observed quantiles manually, but this would not work well if I would like to create plots of multiple groups or using facets, since then I would also need to calculate the observed quantiles manually for each group separately.

            ...

            ANSWER

            Answered 2021-Jun-13 at 20:42

            blogpost mentioned in comments contains a guide to code your own statfunctions to create such plots yourself

            Otherwise, library qqplotr https://aloy.github.io/qqplotr/index.html contains an option detrend=True which basically produce wormplots with accompanying confidence bands.

            If you want lines, and not a band, just do fill=NA, color='black', size=0.5

            Source https://stackoverflow.com/questions/67091084

            QUESTION

            How to double fill a geom_bar with two characteristics
            Asked 2021-Jun-09 at 21:24

            I'm working with house price indices and I have a question on how to add another geom to a ggplot. This is an example data that I made for this question. I have housing data from a census and from online postings. rooms a variable for a housing characteristic (many or few rooms), and value is the percentage of homes for each source that has that characteristic. Then, houses and apts show the percentage of houses and apts that the city has for that data source. So for example, city 1 has 40% houses and 60% apartments in the census data and 45% houses and 55% apartments in the zillow data. I made a geom_bar faceting by rooms and filling by source so I have two plots, one for rooms=1 and another for rooms=2, each one of them with two bars for each city (one for each source). Now, I want to fill those same bars with the percentage of houses and apartments for each city and source.

            I'd be very grateful if someone can help me with this.

            The code I'm currently using for the plot is the following:

            ...

            ANSWER

            Answered 2021-Jun-09 at 21:24

            If I understand correctly, you're looking to kind of separate out and show in one plot the differentiation of:

            • City
            • Rooms
            • Value (the length of the bar here)
            • % houses or % apts (one is the inverse of the other, so basically just showing the same thing)

            If I have that correct, perhaps the simplest way is to just facet across two variables instead of one using facet_grid():

            Source https://stackoverflow.com/questions/67908064

            QUESTION

            geom_segment line vertical for multiple variable plot
            Asked 2021-Jun-07 at 11:26

            The plot code below makes the segment line congverge at the center of the descrete x variable for all colours. What can be done so that the segment line is vertical for each x variable respective of colour?

            ...

            ANSWER

            Answered 2021-Jun-07 at 11:26

            position_dodge() can't handle xend and yend. Use geom_line() or geom_linerange() instead:

            Source https://stackoverflow.com/questions/67869849

            QUESTION

            How to remove percentage breakdowns from a legend created by ggplot2
            Asked 2021-Jun-03 at 14:45

            I have made a plot displaying multiple facets of my data. The colour bar created by scale_colour_gradientn is confusing because it shows percentage breakdowns. Could I get rid of these percentage breakdowns and add my own. I have tried using values and breaks parameters but with no luck. I think maybe ggplot is confused because most of the values are either very small or close to 1. I have added a toy dataset, code and image output below.

            dput(df)

            ...

            ANSWER

            Answered 2021-Jun-03 at 14:45

            Because your Adj.P.value is numeric, you have to break it into categories first.

            Source https://stackoverflow.com/questions/67818483

            QUESTION

            Use Athena SQL to get a value from JSON key
            Asked 2021-Jun-03 at 13:51

            I need to get the email address from this 'facets' table I created from my firehose logs (JSON).

            Now, I am using Athena to get particular information.

            I need to get the email addresses from this:

            This is my out of 'facets' when I pass-

            ...

            ANSWER

            Answered 2021-Jun-03 at 13:51

            Assuming you have one column which stores json in provided format you can use json_extract with needed paths (and maybe some casts):

            Source https://stackoverflow.com/questions/67819368

            QUESTION

            ais-refinement-list in VueInstantSearch(Algolia) doesn't renders list
            Asked 2021-Jun-03 at 11:43

            I have stucked with an issue using refinement list widget of algolia. First of all my resulting data structure is like that:

            ...

            ANSWER

            Answered 2021-Jun-03 at 11:43

            Problem was in Dashboard of Algolia. When we clicked on 'searchable' instead of 'filter only' radiobutton for chosen attributeForFaceting - everything starts working good.

            Source https://stackoverflow.com/questions/67784631

            QUESTION

            Hybris SOLR facet indexed property not showing
            Asked 2021-May-28 at 07:47

            I've created a new SOLR Indexed property that must act as category a facet:

            ...

            ANSWER

            Answered 2021-May-28 at 07:17

            If all the products in the result have the same value or no value at all, the facet won't show. The facet will only appear if it will make a difference in the result when the user filters by it. Can you check if that's the case?

            Source https://stackoverflow.com/questions/67673964

            QUESTION

            GGplot scatterplot color interval
            Asked 2021-May-25 at 22:44

            Im currently getting back into using R, but its been a while so im a little rusty.

            I have the following code for making plots using ggplot2:

            ...

            ANSWER

            Answered 2021-May-25 at 22:44

            If you want to use one color shade for each range of values, you can create a grouping (factor) column with levels on the condition of PAH16Cons values <100, 100-500, or >500. Afterwards, use this column for the color aesthetics in the ggplot and use scale_color_manual(values=c("green", "yellow", "red")) to customize the color.

            Source https://stackoverflow.com/questions/67695247

            QUESTION

            Mean points end up next to boxplot bars
            Asked 2021-May-25 at 11:13

            I'm trying to put a mean in a boxplot with facets but the mean points does not end up on top of the boxplot but next to them. Any suggestions as how to fix this so that the mean points end up on top of the boxplots?

            Here's the code for the ggplot2

            ...

            ANSWER

            Answered 2021-May-25 at 09:05

            You can use position=position_dodge(0.9) like the following code

            Source https://stackoverflow.com/questions/67684043

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

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