Bioinformatics Club: mini R camp for data scientists

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Xianjun Dong

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Jan 11, 2018, 9:38:59 AM1/11/18
to Bioinformatics Club at BWH
Dear all, 

Happy new year of 2018!

I'd like to announce the first event of 2018 from Bioinformatics Club: A six-session mini R camp for data scientists, jointly hosted by Bioinformatics Club and Partners Research Computing. It will cover the most popular R packages for data scientists, including ggplot2, dplyr, reshape2, readr, tidyr, data.table etc. Below is the schedule. You don't want to miss it!

Note: the camp is open to public and limited to 25 seats. First come, first served. Please help to spread around. 

TopicLecturerDateTimePlace
ggplot2 (session 1)Jie HuangFriday, Jan 12, 201811am-12PMBTM vtc 02006B
ggplot2 (session 2)Jie HuangThursday, Jan 18, 201812:00 - 1:00PMBTM 10004
purrr and data.tableTao WangTuesday, Jan 23, 201812:00 - 1:00PMBTM vtc 02006B
dplyrJie HuangTuesday, Jan 30, 201812:00 - 1:00PMBTM vtc 02006B
readr / tibbleHenry PaikTuesday, Feb 6, 201812:00 - 1:00PMBTM vtc 02006B
reshape2 and tidyrXianjun DongMonday, Feb 12, 20181:00 - 2:00PMBTM vtc 02006B

Best,
-Xianjun

BioinformaticsClub.2018Jan.png

Huiyuan Zhang

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Jan 12, 2018, 10:11:43 AM1/12/18
to Bioinformatics Club at BWH
Hello Xianjun,

The minicamp sounds wonderful! Do you require RSVP to join or are seats first come first served for every session?

Best
Huiyuan

Xianjun Dong

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Jan 12, 2018, 10:50:13 AM1/12/18
to Bioinformatics Club at BWH, Xianjun Dong
hi, 

The first talk — ggplot2 (session 1) — will begin in 10 minutes. Again, no registration required. First come, first served. 

Here is the shared slide for today’s talk:

WebEx link for those who cannot come:

Thanks,

Xianjun Dong, PhD
----------------------------------------------------
Director of Computational Neuroscience
Neurogenomics Laboratory and Parkinson Personalized Medicine 
Brigham and Women's Hospital

Instructor in Neurology, Harvard Medical School

Building for Transformative Medicine, 
60 Fenwood Road, 9002EE
Boston, MA 02115


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Dong, Xianjun

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Jan 18, 2018, 8:20:42 AM1/18/18
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Dear all,

Today is Day 2 of our mini R camp: the ggplot (session 2). Jie will first review what we learned in the previous session and then talk about the advanced usage of ggplot grammar with many interesting examples. So please join us regardless you came for session 1 or not. 

Again, no requirement, no registration. 

Note the location will be BTM 10004 (the conference room at BTM building 10th floor). The talk will start at 12:00pm. Please don’t forget to come. 

See you there 

Xianjun 

Sent from my iPhone
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Ling Teng

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Jan 18, 2018, 9:41:24 AM1/18/18
to Dong, Xianjun, Bioinformatics Club at BWH
Hi Xianjun,

Is it possible to attend online as last week?

Thanks,
Ling

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Dong, Xianjun

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Jan 18, 2018, 11:23:30 AM1/18/18
to Ling Teng, Bioinformatics Club at BWH
Yes, we will launch WebEx and you should be able to attend online via the link below:

“See” you soon!

-XD


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Ke Wang

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Jan 18, 2018, 1:28:46 PM1/18/18
to Dong, Xianjun, Ling Teng, Bioinformatics Club at BWH
Hi Xianjun and Jie,

Thank you very much for today's session. I really think it's a very informative training session of ggplot2. So I want to know if it's possible for Jie to share today's slides and the sample codes?

Thank you!

All best,
Ke



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Huang, Jie

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Jan 18, 2018, 1:34:02 PM1/18/18
to Ke Wang, Dong, Xianjun, Ling Teng, Bioinformatics Club at BWH
Hi Ke,

Thank you very much for attending! Here is the slide link:https://docs.google.com/presentation/d/1wt1F3-OQNnbvcqiB7rr0V-FmA6TLeQqtZKOGyYLKVBE/edit#slide=id.gc6f90357f_0_0 On its last page you can find the R code link.

Best,
Jie

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Ke Wang

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Jan 18, 2018, 1:40:44 PM1/18/18
to Huang, Jie, Dong, Xianjun, Ling Teng, Bioinformatics Club at BWH
Hi Jie,

Great. Thank you very much for sharing!

All best,
Ke

Ke Wang
Research Assistant II
Channing Division of Network Medicine
Brigham & Women's Hospital
Boston, MA

Jie


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Huang, Jie

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Jan 18, 2018, 3:47:18 PM1/18/18
to Bioinformatics Club at BWH, Dong, Xianjun
Hi all,

During this morning’s talk, there was an unsolved question: when writing your own functions in R, how to pass a variable as an argument. 

Here I am attaching 4 screenshots from the ggplot2 book (www.ggplot2.org/book). So we need to use one of the four functions: quote(), as.name(), substitute() or parse(). Please read file 1 through file 4 if interested. 

Xianjun, can you forward this email to the guy, if he hasn’t been added to this maillist yet? Thanks!


The code is copied below:

library(ggplot2)
data("mpg")

piechart <- function(data, mapping) { ggplot(data, mapping) +
    geom_bar(width = 1) + coord_polar(theta = "y") + xlab(NULL) +
    ylab(NULL)
}
piechart(mpg, aes(factor(1), fill = class))

# pass variable names directly
piechart1 <- function(data, var, ...) {
  piechart(data, aes_(~factor(1), fill = as.name(var)))
}

piechart2 <- function(data, var, ...) { piechart(data, aes_(~factor(1), fill = var))
}

piechart3 <- function(data, var, ...) {
  piechart(data, aes_(~factor(1), fill = substitute(var)))
}

piechart1(mpg, "class") + theme(legend.position = "none")
piechart2(mpg,~class) + theme(legend.position = "none")
piechart3(mpg, class) + theme(legend.position = "none")


Best,
Jie


Xianjun Dong

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Jan 30, 2018, 8:47:26 AM1/30/18
to Bioinformatics Club at BWH
Dear all,

Today is Day 4 of our mini R camp. Jie Huang will talk about dplyr. dplyr is a very useful package and a must-have for data analysts. So please join us regardless you have R background or not.

Again, no requirement, no registration.

Note the location will be BTM 2006 (the conference room at corner of BTM building 2nd floor). The talk will start at 12:00pm. Please don’t forget to come.

See you there

Xianjun

Xianjun Dong

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Jan 30, 2018, 11:51:17 AM1/30/18
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