Circos plot with heatmap
0
0
Entering edit mode
12 months ago

Hey guys, could someone help me to plot a graph like that? enter image description here Basically, it is a chordDiagram (or a heatmap with links) performed in circlize in R. It shows how many genes are shared between three conditions (gray, purple, and orange) and the fold-change of each protein in each condition (heatmap). For a long time, I have tried several approaches to perform a picture like that using the circlize book. However, I am not being able to find the adjacency matrix that allows joining heatmap and chordDiagrams.

I've tried this code below but is far from what I want

df1 = structure(list(gene name = c("WDR7", "MT-ND5", "STK32C", "CAMK1D", "TXNL1", "AMOTL2", "TRMT10C", "DNAJC6", "REC8", "ARPC1A", "CADM2", "CORO1C", "CCDC150", "MAT2A", "SYT1", "UBE2Q1", "GDAP1L1", "RCN2", "MYO5A", "NCAN", "MBOAT7", "PPP2R5E", "MARK1", "EEF1A1", "HSPA9", "HSPA4", "PGD", "SIRPB1", "ANK3", "HNRNPR", "SMARCE1", "MARS", "CNTNAP1", "ANK2", "HIRIP3", "PDHA1", "CD81", "PCMT1", "SOGA3", "FLT1", "ABCB6", "MARCKS", "PIP5K1C", "ATP6V1A", "TOMM70", "HNRNPA3", "AGAP3", "BCAP31", "GATM", "RAP1GDS1", "ABCB8", "SERPINI1", "TTYH2", "FSCN1", "CYFIP2", "MAP2K4", "DCTN1", "DPH2", "WDR37", "MYH9", "ORC4", "PRDM11", "SACM1L", "NDUFS2", "HSP90AB3P", "ACAT1", "LRRC10B", "ATP6V0D1", "VAT1", "AKR1B1", "SFXN1", "RAB14", "ADAM22", "HSP90AA1", "ACTN4", "CCT2", "ACTR3", "TBC1D24", "PLEC", "SNX30", "PDIA6", "SIRPB1", "MSN", "TRIM2", "TERF2", "DPYSL4", "PTK6", "USO1", "CCT7", "ATCAY", "APP", "LDHA", "GAS7", "RAP2C", "ATIC", "CLTC", "DSTN", "CCT5", "SFN", "CPNE8"), log2(fc) = c(-0.753889084089214, -2.42317308944667, 0.706950397193475, -1.32387351817766, 0.755066088255367, 0.555981293669421, 1.07151530578741, 0.591299787820189, 0.762728631457299, -1.90944847128428, 0.726900878368743, 1.03129422108257, 0.785598246520011, -1.16262324298186, 0.930874575346298, -1.18786532056107, -2.04676689534369, -2.30463459029556, 0.708478002279652, 0.467631731585401, 0.704524913373953, 0.600227804580048, 1.91719419620395, -1.11478618903213, 0.854240624505702, 1.14907724884474, 0.696259752337004, 0.627499184068163, 0.891441855450337, -1.50269393783596, 0.710050499119398, -2.17603882218045, 0.685445415738682, 0.515928331645937, 1.270360199852, -0.946591407172443, -2.66567109722171, -3.01788325905002, 0.695781494964899, -1.36639412981052, 0.622892431280113, 0.958471320608125, 0.883949128904109, -0.834748258558578, -1.50134098750353, 0.81310895014144, 0.670392364405923, -1.74747489050681, -1.75151599577174, -0.933953810555048, 0.518810017983056, 0.641372767054202, -1.30418703581051, 0.838677464283049, 0.586852512976649, -4.87469230868739, 1.0371358774387, 1.88076558607344, 0.578140946621983, -1.05864400336003, -1.77946502478341, -1.27518412880707, 1.36586823931134, -0.993287714573033, 1.17402831678954, -1.15262144056542, 1.15456114364791, 0.921320553744132, -1.64192666940235, 0.535390707305041, 0.610464757774085, -1.02486275302797, 0.908390820566128, 0.680881761546337, 0.600863379739068, -1.98430870180797, -0.539616640152833, -4.78715977351774, 0.935283686990914, -0.451076745070576, -0.843208118143084, 0.42068119425579, 1.06935805604975, -0.884431480512012, 1.20653594138675, -0.645690820983503, 0.897034451874006, 1.11054352416216, 0.658201759659289, 0.603594448587426, 0.892744752142811, 1.06185657509095, -0.797800870871172, 0.443490145658938, 0.473110560770304, 1.08645016126984, 0.685208841193547, -0.512927090296666, 0.381962745708941, -0.343115196814253)), row.names = c(NA, -100L), class = c("tbl_df", "tbl", "data.frame"))

df2 = structure(list(gene name = c("AKR1B1", "PPIB", "SYNGR3", "ERMN", "PSMC1", "RCN2", "IGF2BP2", "RGS2", "MYO5A", "EEF1A1", "GFAP", "NEFL", "SERPINB11", "SNX30", "PPP3CB", "EPB41L3", "TPM3", "TRIM2", "UGP2", "ANK2", "PSMC3", "AQP4", "MAT2A", "ADSS", "DPYSL4", "ANK3", "WDR37", "CCDC39", "SMG1", "NCAM2", "YWHAZ", "ST13", "RHOT1", "SCRN1", "HLA-B", "SLC4A10", "PGD", "DNAJC6", "STAM", "PRRT2", "TUBB6", "PGRMC1", "ADH5", "OXCT1", "EHD1", "RPL18", "PCMT1", "MBP", "OGDHL", "EHD4", "HNRNPK", "KIF5C", "AIF1L", "MAP6", "MPP2", "PTPRS", "ACTR3", "ATP6V1A", "NAP1L1", "RAP1A", "RC3H1", "FLT1", "HIP1R", "GNAT1", "FAM49B", "L1CAM", "DLD", "GDAP1L1", "KIF5B", "NCKAP1", "ASAH2", "C2orf73", "AP3D1", "MARCKS", "SLC32A1", "CA4", "ACAD9", "UBXN6", "AK3", "SHISA6", "ECPAS", "SIRPG", "NCAN", "GATM", "CAPZB", "SKP2", "SARS", "BLZF1", "PFKL", "CCT6A", "TUBB2A", "GSS", "PTK6", "HACD3", "PDGFRA", "DBN1", "ENDOD1", "NME1", "GLS", "CYB5R3"), log2(fc) = c(0.598333952254718, 0.153463756560596, 0.887551875841772, 0.091959632261785, -0.0653121766624924, -3.56868763094616, 0.151948529510218, -1.40501441288204, 0.659460131614942, -1.21884542665894, -1.51495771291409, 0.15320013183262, -0.235333915730733, -0.72267258178632, 0.0817143948992161, 0.194161532997957, -0.847547076448773, -0.5542565675026, 0.449903870369007, 0.537817497798565, 0.0131201739987223, -1.87812410797283, -1.74304031216728, 0.0428654560104417, -0.506263874308884, 1.01852827484186, 0.79297848164945, 0.505699531169215, 0.390840222442379, 0.231025596170127, 0.814773065515411, -0.788792340159321, 1.00357708867338, -0.225959588795074, -0.604063590055194, 0.101323305946575, 0.598637301986858, 0.448735012322506, -0.434051480487214, 0.509370920933677, -1.33972080518329, -0.466794002719205, 0.085298636583007, -0.341141638674929, -0.291258163654605, 0.275087788598648, -2.88329845512312, 0.147721317067099, 0.353761552206854, 0.350811986771419, -0.836858004334406, -1.64208295811383, 3.30720378286184, 0.128366292219461, -0.298094602713737, -0.722486254014747, -0.31392157790986, -0.989970566852713, -0.323114200303385, 0.00187153274466455, -0.716425438308338, -1.36796743209534, 0.110829790241314, 2.30616564069286, -0.604790315926423, 0.52056074847418, -0.119901119018495, -2.84777558540338, -0.0804988543984884, -0.114889636807043, 1.70299513255115, -0.171144406165986, -0.457142571344917, 0.650438672428674, 0.619043201604299, 0.453529906597265, 1.1503297642025, -0.484740805322257, 0.0458622216893329, 0.063287395797108, 0.038303102157864, 0.316472564305251, 0.371553433527815, -2.43298250813505, -1.13283043658811, 0.146298315295601, -1.50905987947572, 0.542832967114625, 0.288385695594898, -1.50721460279777, -0.644837011658615, 0.931651340453037, 0.926562624101868, 0.28734030063008, -0.615855595778433, 0.442046670786553, -0.88920850234374, -0.409096169339377, 0.40133744826533, -0.761762583856793)), row.names = c(NA, -100L), class = c("tbl_df", "tbl", "data.frame"))

list <- list(df, df2)

ptn <- sapply(seq_len(length(list)), function(x)
sapply(seq_len(length(list)), function(y) length(intersect(unlist(list[x]), unlist(list[y]))))) row.names(ptn) <- c('df', 'df2', 'df3') colnames(ptn) <- c('df', 'df2') for (c in 1:3){ for (l in 1:2){ if(c>=l){ptn[l,c] <- NA} } }

library(circlize); chordDiagram(ptn, annotationTrack = c('name', 'grid'))

Could you help me with a general code to perform the image like that?

R Circlize heatmap chordDiagram • 389 views
ADD COMMENT
1
Entering edit mode

Check the methylation example in circlize.

ADD REPLY
0
Entering edit mode

Your example has errors so it;'s hard to reproduce. The first is you have a space in gene name and the second is log2(fc) is a function so it will return an error. Change both to log2FC and gene_name. The second issue I ran across is the for loop returns out of bounds because you have 1:3 when you only have 2 data frames (and also the row names are too long?). Here it is corrected:

ptn <- sapply(seq_len(length(list)), function(x) sapply(seq_len(length(list)), function(y) length(intersect(unlist(list[x]), unlist(list[y])))))

row.names(ptn) <- c('df', 'df2') 
colnames(ptn) <- c('df', 'df2') 
for (c in 1:2){ 
  for (l in 1:2){ 
    if(c>=l){ 
      ptn[l,c] <- NA
    }
    }
  }
ADD REPLY

Login before adding your answer.

Traffic: 1468 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6