[IGBF-3257] Adding UpSetR on to the end of the EBSeq-HMM pipeline - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Minor
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
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Story Points:
1
Epic Link:
Support NSF pollen grant
Sprint:
Spring 3 2023 Feb 1

Description

We want to get Venn Diagram like results for the time series data created via EBSeq-HMM.
We wish to use UpsetR for it's fancy visualization.

Example on how to run UpsetR in R:

{{library(UpSetR)

myGeneSets <- list(
set1 = c("gene1","gene2","gene3"),
set2 = c("gene1","gene4","gene5", "gene7"),
set3 = c("gene1","gene7")
)

upset(fromList(myGeneSets))}}

Run this on the Johnson time series data.

A good location for the ebseq data to go , along with these results would be at the following
Google drive location.

Location for the data on Google Drive:
https://drive.google.com/drive/folders/1_I6PLSoBg4H3Y1MzY2qhxjk-FBmM4cmQ?usp=share_link

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V2_UpsetR.png
15/Feb/23 3:54 PM
153 kB
Molly Davis
Up-Up-Up_upsetR.png
15/Feb/23 5:44 PM
109 kB
Molly Davis
upsetR_distinct.png
15/Feb/23 5:05 PM
163 kB
Molly Davis
up_up_up_upsetR.pdf
17/Feb/23 11:45 AM
30 kB
Molly Davis
up_up_down_upsetR.pdf
17/Feb/23 11:45 AM
30 kB
Molly Davis
up_down_up_upsetR.pdf
17/Feb/23 11:45 AM
37 kB
Molly Davis
up_down_down_upsetR.pdf
17/Feb/23 11:45 AM
31 kB
Molly Davis
down_up_up_upsetR.pdf
17/Feb/23 11:45 AM
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Molly Davis
down_up_down_upsetR.pdf
17/Feb/23 11:45 AM
37 kB
Molly Davis
down_down_up_upsetR.pdf
17/Feb/23 11:45 AM
33 kB
Molly Davis
down_down_down_upsetR.pdf
17/Feb/23 11:45 AM
27 kB
Molly Davis
all_upsetR.png
15/Feb/23 2:33 PM
147 kB
Molly Davis
all_upsetR.pdf
17/Feb/23 11:45 AM
38 kB
Molly Davis

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Molly Davis added a comment - 17/Feb/23 10:26 AM - edited

Add title to each PDF file and then update bitbucket and google drive location.

Bitbucket Commit: https://bitbucket.org/hotpollen/time-series/commits/d286927563f67e7b3c7e70ba5529225ca65d30b2

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Molly Davis added a comment - 17/Feb/23 10:26 AM - edited Add title to each PDF file and then update bitbucket and google drive location. Bitbucket Commit: https://bitbucket.org/hotpollen/time-series/commits/d286927563f67e7b3c7e70ba5529225ca65d30b2

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Molly Davis added a comment - 16/Feb/23 4:59 PM - edited

Bitbucket updated with UpsetR

Commit: https://bitbucket.org/hotpollen/time-series/commits/412b14b00958ec96ff995265fab2fd378dbf63cf

Next step: need to update google drive with new files after Dr. Reid reviews.

[~RobertReid]

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Molly Davis added a comment - 16/Feb/23 4:59 PM - edited Bitbucket updated with UpsetR Commit: https://bitbucket.org/hotpollen/time-series/commits/412b14b00958ec96ff995265fab2fd378dbf63cf Next step: need to update google drive with new files after Dr. Reid reviews. [~RobertReid]

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Molly Davis added a comment - 15/Feb/23 5:44 PM - edited

Update UpsetR:

Code:

library(UpSetR)

myGeneSets <- list(Heinz_control = c(hcdf1$SL5_gene_name),
Heinz_stress = c(hsdf1$SL5_gene_name),
Nagcarlang_control = c(ncdf1$SL5_gene_name), 
Nagcarlang_stress = c(nsdf1$SL5_gene_name),
Tamaulipas_control = c(tcdf1$SL5_gene_name),
Tamaulipas_stress = c(tsdf1$SL5_gene_name)
)
all_upsetR <- upset(sets = c("Heinz_control", "Heinz_stress", "Nagcarlang_control", "Nagcarlang_stress", "Tamaulipas_control", "Tamaulipas_stress"),  keep.order = T ,nsets = 6, fromList(myGeneSets), main.bar.color = 'navy', sets.bar.color = 'navy', shade.color = "navy", shade.alpha = .3, text.scale = c(1.3, 1.3, 1, 1, 1, 0.75),line.size = 1)
all_upsetR

I just included the Up-Up-Up Genes for this next one

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Molly Davis added a comment - 15/Feb/23 5:44 PM - edited Update UpsetR: Code: library(UpSetR) myGeneSets <- list(Heinz_control = c(hcdf1$SL5_gene_name), Heinz_stress = c(hsdf1$SL5_gene_name), Nagcarlang_control = c(ncdf1$SL5_gene_name), Nagcarlang_stress = c(nsdf1$SL5_gene_name), Tamaulipas_control = c(tcdf1$SL5_gene_name), Tamaulipas_stress = c(tsdf1$SL5_gene_name) ) all_upsetR <- upset(sets = c( "Heinz_control" , "Heinz_stress" , "Nagcarlang_control" , "Nagcarlang_stress" , "Tamaulipas_control" , "Tamaulipas_stress" ), keep.order = T ,nsets = 6, fromList(myGeneSets), main.bar.color = 'navy', sets.bar.color = 'navy', shade.color = "navy" , shade.alpha = .3, text.scale = c(1.3, 1.3, 1, 1, 1, 0.75),line.size = 1) all_upsetR I just included the Up-Up-Up Genes for this next one

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Molly Davis added a comment - 15/Feb/23 5:01 PM - edited

UpsetR uses distinct not intersect. Need to use different function.

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Molly Davis added a comment - 15/Feb/23 5:01 PM - edited UpsetR uses distinct not intersect. Need to use different function.

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Molly Davis added a comment - 15/Feb/23 4:58 PM

Printing Intersections:

intersect(Heinz_control_df$SL5_gene_name,Heinz_stress_df$SL5_gene_name)

 [1] "Solyc06G001408" "Solyc09G002778" "Solyc12G002726" "Solyc06G000062" "Solyc04G000530" "Solyc07G002715" "Solyc06G002665" "PRAM_26139"    
  [9] "Solyc05G001386" "Solyc03G002252" "Solyc11G000303" "Solyc08G001590" "Solyc06G000126" "Solyc09G002278" "Solyc04G002962" "Solyc11G001387"
 [17] "Solyc10G000812" "Solyc03G000065" "Solyc08G001723" "Solyc06G001573" "Solyc08G000122" "Solyc01G002437" "Solyc04G000302" "Solyc04G001838"
 [25] "Solyc03G003220" "Solyc03G003450" "Solyc02G002349" "Solyc03G003579" "Solyc01G004383" "Solyc06G000207" "Solyc12G000235" "Solyc06G000063"
 [33] "Solyc08G001779" "PRAM_129002"    "Solyc01G003828" "Solyc02G002445" "Solyc08G001192" "Solyc10G002570" "Solyc12G000103" "Solyc06G001783"
 [41] "Solyc11G002395" "Solyc01G001722" "Solyc07G002695" "Solyc01G004183" "Solyc01G004163" "Solyc01G002277" "Solyc09G000029" "Solyc04G000344"
 [49] "Solyc10G002465" "Solyc09G001939" "Solyc01G004397" "Solyc07G000083" "Solyc04G000622" "Solyc03G000156" "Solyc01G003972" "Solyc02G002189"
 [57] "Solyc02G000293" "Solyc12G000269" "Solyc11G001089" "Solyc11G001449" "Solyc03G001292" "Solyc03G003043" "Solyc06G001100" "Solyc03G001766"
 [65] "Solyc08G000939" "Solyc08G002155" "Solyc06G000003" "Solyc09G001902" "Solyc12G002543" "Solyc11G000089" "Solyc06G001587" "Solyc01G002400"
 [73] "Solyc10G001592" "Solyc06G001502" "Solyc08G001829" "Solyc05G002060" "Solyc07G002217" "Solyc05G002516" "Solyc07G000007" "Solyc06G000253"
 [81] "Solyc11G000653" "Solyc04G002972" "Solyc08G000931" "Solyc01G003310" "Solyc02G001998" "Solyc01G002505" "Solyc03G001618" "Solyc06G000888"
 [89] "Solyc01G003475" "Solyc03G002604" "Solyc07G000076" "Solyc09G002599" "Solyc03G000179" "Solyc01G002587" "Solyc04G002343" "Solyc12G002299"
 [97] "Solyc08G002364" "Solyc07G001362" "Solyc07G002692" "Solyc08G001759" "Solyc09G000979" "Solyc07G001635" "Solyc12G000797" "Solyc03G002677"
[105] "Solyc12G000320" "Solyc02G001956" "Solyc11G001805" "Solyc11G001719" "Solyc12G000409" "Solyc12G002815" "Solyc03G002982" "Solyc01G000031"
[113] "Solyc01G002252" "PRAM_15614"     "Solyc04G001498" "Solyc02G001499" "Solyc10G001075" "Solyc07G000771" "Solyc02G002340" "Solyc08G000176"
[121] "Solyc05G001884" "Solyc10G001081" "Solyc02G001188" "Solyc01G002659" "Solyc10G000147" "Solyc04G000037" "Solyc07G002631" "Solyc04G000132"
[129] "Solyc04G002577" "Solyc11G000153" "Solyc03G001217" "Solyc05G000793" "Solyc09G002844" "Solyc04G000076" "Solyc08G002520" "Solyc07G000186"
[137] "Solyc02G001859" "Solyc06G001226" "Solyc12G002711" "Solyc12G001312" "Solyc03G001683" "Solyc04G001971" "Solyc02G001532" "Solyc08G000929"
[145] "Solyc07G001816" "Solyc02G001368" "Solyc09G000933" "Solyc11G000937" "Solyc09G002102" "Solyc06G002098" "Solyc05G000446" "Solyc11G001980"
[153] "Solyc00G000016" "Solyc03G001774" "Solyc08G000410" "Solyc06G002366" "Solyc01G001733" "Solyc08G000257" "Solyc12G002430" "PRAM_25885"    
[161] "Solyc01G000248" "Solyc11G002413" "Solyc04G001129" "Solyc09G000217" "Solyc07G000014" "Solyc10G002821" "Solyc06G000480" "Solyc01G001978"
[169] "Solyc04G003009" "Solyc02G001707" "Solyc04G000723" "Solyc10G001481" "Solyc02G001042" "Solyc03G002264" "Solyc01G002661" "Solyc08G001514"
[177] "Solyc02G002712" "Solyc07G002433" "Solyc09G002252" "Solyc01G003109" "Solyc08G001461" "Solyc09G002351" "Solyc04G002719" "Solyc12G001921"
[185] "Solyc01G002783" "Solyc07G000911" "PRAM_128428"    "Solyc10G000380" "Solyc05G000191" "Solyc04G002090" "Solyc05G000770" "Solyc10G000273"
[193] "Solyc02G001108" "Solyc07G001532" "Solyc11G001549" "Solyc03G000494" "Solyc07G002229" "Solyc01G002665" "Solyc05G002452" "Solyc03G002298"
[201] "Solyc08G000678" "Solyc02G002650" "Solyc11G001702" "Solyc00G000015" "Solyc05G000066" "Solyc08G000020" "Solyc04G002358" "Solyc12G001493"
[209] "Solyc10G000538" "Solyc01G002367" "Solyc11G001236" "Solyc03G002907" "Solyc12G001846" "Solyc04G000072" "Solyc01G001855" "Solyc03G002916"
[217] "Solyc02G002500" "Solyc10G000383" "Solyc03G002992" "Solyc03G000091" "Solyc06G001369" "Solyc09G001945" "Solyc06G001881" "Solyc06G001394"
[225] "Solyc10G000244" "Solyc07G000255" "Solyc05G000389" "Solyc04G002021" "Solyc02G002045" "Solyc06G000025" "Solyc10G000015" "Solyc10G001671"
[233] "Solyc01G000486" "Solyc07G001943" "Solyc06G002530" "Solyc03G003313" "Solyc11G000362" "Solyc04G002616" "Solyc08G001274" "Solyc06G002677"
[241] "Solyc09G002686" "Solyc01G000190" "Solyc08G000223" "Solyc03G001423" "Solyc12G000961" "Solyc00G000048" "Solyc01G003029" "Solyc01G004304"
[249] "Solyc00G000012" "Solyc01G001715" "Solyc01G002782" "Solyc07G001475" "Solyc10G001763" "Solyc07G002580" "Solyc06G002044" "Solyc05G000640"
[257] "Solyc02G001142"

Comment: Not the same number as UpsetR graph.

Show

Molly Davis added a comment - 15/Feb/23 4:58 PM Printing Intersections: intersect(Heinz_control_df$SL5_gene_name,Heinz_stress_df$SL5_gene_name) [1] "Solyc06G001408" "Solyc09G002778" "Solyc12G002726" "Solyc06G000062" "Solyc04G000530" "Solyc07G002715" "Solyc06G002665" "PRAM_26139" [9] "Solyc05G001386" "Solyc03G002252" "Solyc11G000303" "Solyc08G001590" "Solyc06G000126" "Solyc09G002278" "Solyc04G002962" "Solyc11G001387" [17] "Solyc10G000812" "Solyc03G000065" "Solyc08G001723" "Solyc06G001573" "Solyc08G000122" "Solyc01G002437" "Solyc04G000302" "Solyc04G001838" [25] "Solyc03G003220" "Solyc03G003450" "Solyc02G002349" "Solyc03G003579" "Solyc01G004383" "Solyc06G000207" "Solyc12G000235" "Solyc06G000063" [33] "Solyc08G001779" "PRAM_129002" "Solyc01G003828" "Solyc02G002445" "Solyc08G001192" "Solyc10G002570" "Solyc12G000103" "Solyc06G001783" [41] "Solyc11G002395" "Solyc01G001722" "Solyc07G002695" "Solyc01G004183" "Solyc01G004163" "Solyc01G002277" "Solyc09G000029" "Solyc04G000344" [49] "Solyc10G002465" "Solyc09G001939" "Solyc01G004397" "Solyc07G000083" "Solyc04G000622" "Solyc03G000156" "Solyc01G003972" "Solyc02G002189" [57] "Solyc02G000293" "Solyc12G000269" "Solyc11G001089" "Solyc11G001449" "Solyc03G001292" "Solyc03G003043" "Solyc06G001100" "Solyc03G001766" [65] "Solyc08G000939" "Solyc08G002155" "Solyc06G000003" "Solyc09G001902" "Solyc12G002543" "Solyc11G000089" "Solyc06G001587" "Solyc01G002400" [73] "Solyc10G001592" "Solyc06G001502" "Solyc08G001829" "Solyc05G002060" "Solyc07G002217" "Solyc05G002516" "Solyc07G000007" "Solyc06G000253" [81] "Solyc11G000653" "Solyc04G002972" "Solyc08G000931" "Solyc01G003310" "Solyc02G001998" "Solyc01G002505" "Solyc03G001618" "Solyc06G000888" [89] "Solyc01G003475" "Solyc03G002604" "Solyc07G000076" "Solyc09G002599" "Solyc03G000179" "Solyc01G002587" "Solyc04G002343" "Solyc12G002299" [97] "Solyc08G002364" "Solyc07G001362" "Solyc07G002692" "Solyc08G001759" "Solyc09G000979" "Solyc07G001635" "Solyc12G000797" "Solyc03G002677" [105] "Solyc12G000320" "Solyc02G001956" "Solyc11G001805" "Solyc11G001719" "Solyc12G000409" "Solyc12G002815" "Solyc03G002982" "Solyc01G000031" [113] "Solyc01G002252" "PRAM_15614" "Solyc04G001498" "Solyc02G001499" "Solyc10G001075" "Solyc07G000771" "Solyc02G002340" "Solyc08G000176" [121] "Solyc05G001884" "Solyc10G001081" "Solyc02G001188" "Solyc01G002659" "Solyc10G000147" "Solyc04G000037" "Solyc07G002631" "Solyc04G000132" [129] "Solyc04G002577" "Solyc11G000153" "Solyc03G001217" "Solyc05G000793" "Solyc09G002844" "Solyc04G000076" "Solyc08G002520" "Solyc07G000186" [137] "Solyc02G001859" "Solyc06G001226" "Solyc12G002711" "Solyc12G001312" "Solyc03G001683" "Solyc04G001971" "Solyc02G001532" "Solyc08G000929" [145] "Solyc07G001816" "Solyc02G001368" "Solyc09G000933" "Solyc11G000937" "Solyc09G002102" "Solyc06G002098" "Solyc05G000446" "Solyc11G001980" [153] "Solyc00G000016" "Solyc03G001774" "Solyc08G000410" "Solyc06G002366" "Solyc01G001733" "Solyc08G000257" "Solyc12G002430" "PRAM_25885" [161] "Solyc01G000248" "Solyc11G002413" "Solyc04G001129" "Solyc09G000217" "Solyc07G000014" "Solyc10G002821" "Solyc06G000480" "Solyc01G001978" [169] "Solyc04G003009" "Solyc02G001707" "Solyc04G000723" "Solyc10G001481" "Solyc02G001042" "Solyc03G002264" "Solyc01G002661" "Solyc08G001514" [177] "Solyc02G002712" "Solyc07G002433" "Solyc09G002252" "Solyc01G003109" "Solyc08G001461" "Solyc09G002351" "Solyc04G002719" "Solyc12G001921" [185] "Solyc01G002783" "Solyc07G000911" "PRAM_128428" "Solyc10G000380" "Solyc05G000191" "Solyc04G002090" "Solyc05G000770" "Solyc10G000273" [193] "Solyc02G001108" "Solyc07G001532" "Solyc11G001549" "Solyc03G000494" "Solyc07G002229" "Solyc01G002665" "Solyc05G002452" "Solyc03G002298" [201] "Solyc08G000678" "Solyc02G002650" "Solyc11G001702" "Solyc00G000015" "Solyc05G000066" "Solyc08G000020" "Solyc04G002358" "Solyc12G001493" [209] "Solyc10G000538" "Solyc01G002367" "Solyc11G001236" "Solyc03G002907" "Solyc12G001846" "Solyc04G000072" "Solyc01G001855" "Solyc03G002916" [217] "Solyc02G002500" "Solyc10G000383" "Solyc03G002992" "Solyc03G000091" "Solyc06G001369" "Solyc09G001945" "Solyc06G001881" "Solyc06G001394" [225] "Solyc10G000244" "Solyc07G000255" "Solyc05G000389" "Solyc04G002021" "Solyc02G002045" "Solyc06G000025" "Solyc10G000015" "Solyc10G001671" [233] "Solyc01G000486" "Solyc07G001943" "Solyc06G002530" "Solyc03G003313" "Solyc11G000362" "Solyc04G002616" "Solyc08G001274" "Solyc06G002677" [241] "Solyc09G002686" "Solyc01G000190" "Solyc08G000223" "Solyc03G001423" "Solyc12G000961" "Solyc00G000048" "Solyc01G003029" "Solyc01G004304" [249] "Solyc00G000012" "Solyc01G001715" "Solyc01G002782" "Solyc07G001475" "Solyc10G001763" "Solyc07G002580" "Solyc06G002044" "Solyc05G000640" [257] "Solyc02G001142" Comment: Not the same number as UpsetR graph.

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Molly Davis added a comment - 15/Feb/23 2:06 PM - edited

UpsetR Code:

library(UpSetR)

myGeneSets <- list(Heinz_control = c(Heinz_control_df$SL5_gene_name),
Heinz_stress = c(Heinz_stress_df$SL5_gene_name),
Nagcarlang_control = c(Nagcarlang_control_df$SL5_gene_name), 
Nagcarlang_stress = c(Nagcarlang_stress_df$SL5_gene_name),
Tamaulipas_control = c(Tamaulipas_control_df$SL5_gene_name),
Tamaulipas_stress = c(Tamaulipas_stress_df$SL5_gene_name)
)
all_upsetR<-upset(nsets = 6,fromList(myGeneSets), main.bar.color = 'purple', sets.bar.color = 'purple', mb.ratio = c(0.5, 0.5))
all_upsetR

UpsetR Results:

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Molly Davis added a comment - 15/Feb/23 2:06 PM - edited UpsetR Code: library(UpSetR) myGeneSets <- list(Heinz_control = c(Heinz_control_df$SL5_gene_name), Heinz_stress = c(Heinz_stress_df$SL5_gene_name), Nagcarlang_control = c(Nagcarlang_control_df$SL5_gene_name), Nagcarlang_stress = c(Nagcarlang_stress_df$SL5_gene_name), Tamaulipas_control = c(Tamaulipas_control_df$SL5_gene_name), Tamaulipas_stress = c(Tamaulipas_stress_df$SL5_gene_name) ) all_upsetR<-upset(nsets = 6,fromList(myGeneSets), main.bar.color = 'purple', sets.bar.color = 'purple', mb.ratio = c(0.5, 0.5)) all_upsetR UpsetR Results:

People

Assignee:

Molly Davis

Reporter:

Robert Reid

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Dates

Created:

10/Feb/23 1:31 PM

Updated:

17/Feb/23 11:46 AM

Resolved:

17/Feb/23 11:46 AM