Entering edit mode
4.2 years ago
Dracaena
▴
50
Hi guys,
I have ran into some troubles making a population graph using popgraph/ggplot in R. More specifically, I want each module in a different color and I try to do so using geom_edgeset(color = module) and scale_colors_manual( values = nodecolors). What happens is that every node just colors black. How do I solve this issue?
Here is the script I used:
p <- ggplot()
world <- map_data("world") #add a base map = bottom layer
p <- p + geom_polygon(data = world, aes(x=long, y = lat, group=group), fill="lightgrey")
nodecolors <- c("module1" = "yellow", "module2"="green", "module3"="blue", "module4" = "purple") #named chr for colors
p <- p + geom_edgeset( aes(x=longitude,y=latitude), combo, color="darkgrey") #combo is a popgraph/igraph object, an edge matrix decorated with information for each population (such as to which module it belongs)
p <- p + geom_nodeset(aes(x=longitude,y=latitude,color = as.factor(module)), combo, size=mod$nalleles/15)
p <- p + theme(panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_line(colour = "black")) #remove bg
p <- p + scale_color_manual(values = nodecolors)
p
What I get:
here is summary(combo)
IGRAPH 43ff52a UNW- 119 615 --
+ attr: name (v/c), population (v/n), module (v/n), color (v/n), connectivity (v/n), participation (v/n),
| role (v/n), longitude (v/n), latitude (v/n), nalleles (v/n), Hexp (v/n), Hobs (v/n), weight (e/n)
and here is dput(head(combo):
new("dgCMatrix", i = c(2L, 4L, 5L, 0L, 3L, 2L, 0L, 5L, 0L, 4L,
0L, 2L, 3L, 0L, 2L, 0L, 0L, 5L, 1L, 4L, 3L, 1L, 1L, 0L, 3L, 4L,
4L, 5L, 1L, 2L, 1L, 0L, 3L, 3L, 4L, 5L, 1L, 2L, 5L, 3L, 4L, 0L,
2L, 5L, 1L, 0L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 1L, 1L, 2L, 1L, 2L,
3L, 3L, 5L, 3L), p = c(0L, 3L, 3L, 5L, 6L, 8L, 10L, 13L, 15L,
16L, 18L, 20L, 21L, 21L, 21L, 21L, 22L, 23L, 24L, 26L, 26L, 28L,
28L, 30L, 31L, 33L, 36L, 39L, 41L, 44L, 45L, 47L, 53L, 53L, 54L,
56L, 58L, 58L, 58L, 58L, 58L, 58L, 58L, 58L, 58L, 58L, 58L, 58L,
58L, 58L, 58L, 58L, 58L, 58L, 58L, 58L, 58L, 58L, 58L, 59L, 59L,
59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L,
59L, 59L, 59L, 60L, 60L, 60L, 60L, 60L, 61L, 61L, 61L, 61L, 61L,
61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L,
61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L, 61L,
61L, 61L, 62L, 62L, 62L, 62L, 62L), Dim = c(6L, 119L), Dimnames = list(
c("SSA_Ben_Kor_2006", "SSA_Bot_Tut_2009", "SSA_Cam_Ess_2005",
"SSA_Con_Luk_2007", "SSA_Gha_Dal_2009", "SSA_Gha_Mam_2009"
), c("SSA_Ben_Kor_2006", "SSA_Bot_Tut_2009", "SSA_Cam_Ess_2005",
"SSA_Con_Luk_2007", "SSA_Gha_Dal_2009", "SSA_Gha_Mam_2009",
"SSA_Ivo_Abi_2009", "SSA_Ivo_Kor_2005", "SSA_Ivo_Sin_2009",
"SSA_Ken_Riu_1995", "SSA_Mal_Lil_2010", "SSA_Mau_Eas_2010",
"SSA_Mau_Nor_2010", "SSA_Mau_Sou_2010", "SSA_Mau_Wes_2010",
"SSA_Moz_Map_2009", "SSA_Moz_Mec_2008", "SSA_Moz_Mit_2008",
"SSA_Nig_Nig_1991", "SSA_Reu_Lig_2009", "SSA_SAf_Bon_2010",
"SSA_SAf_Cer_2010", "SSA_SAf_Rie_2010", "SSA_SAf_Wol_2010",
"SSA_Sen_Fil_2010", "SSA_Sen_Keu_2010", "SSA_Sen_Thi_2010",
"SSA_Sud_Gez_2009", "SSA_Sud_Sin_2009", "SSA_Tan_Kib_2009",
"SSA_Tog_Ago_2009", "SSA_Tog_Lom_2009", "SSA_Uga_Kaw_2005",
"SSA_Zam_Maz_2008", "SSA_Zam_Lus_2007", "SSA_Zam_Sia_2008",
"EUM_Boz_Mos_2009", "EUM_Boz_Ner_2009", "EUM_Cro_Dub_2009",
"EUM_Cro_Zad_2009", "EUM_Gre_Yol_2009", "EUM_Isr_Kfa_2009",
"EUM_Isr_Kvu_2009", "EUM_Isr_Par_2009", "EUM_Isr_Reh_2009",
"EUM_Isr_Nes_2009", "EUM_Ita_Sic_1998", "EUM_Ita_Met_1996",
"EUM_Ita_Cut_2010", "EUM_Mad_Mad_2011", "EUM_Mon_Bao_2009",
"EUM_Mon_Bar_2009", "EUM_Mon_Las_2009", "EUM_Mor_Mar_2009",
"EUM_Por_Mad_2005", "EUM_Por_Alg_2011", "EUM_Spa_Ali_2010",
"EUM_Spa_Alm_2010", "EUM_Spa_Cas_2010", "EUM_Spa_Val_2010",
"EUM_Spa_Bal_2010", "EUM_Tun_NA_NA", "EUM_Tur_Bom_2010",
"HAW_Haw_Haw_1991", "HAW_Haw_Kip_1991", "HAW_Haw_Kau_1991",
"HAW_Haw_Oah_1991", "HAW_Haw_Mau_1991", "CAM_Cos_Ala_1992",
"CAM_Cos_Gua_1993", "CAM_Cos_San_1956", "CAM_Cos_Pun_1992",
"CAM_ElS_San_1998", "CAM_Gua_San_2009", "CAM_Gua_Gua_1997",
"CAM_Gua_Gua_1999", "CAM_Gua_San_1990", "CAM_Gua_Ant_1990",
"CAM_Hon_Hon_NA", "CAM_Hon_IH_2000", "CAM_Hon_Tru_2010",
"CAM_Hon_Hon_1992", "CAM_Hon_Riv_2000", "CAM_Nic_Leo_2000",
"CAM_Nic_Man_2000", "CAM_Nic_Riv_2000", "CAM_Pan_Chi_2009",
"CAM_Pan_Pan_1992", "SAM_Arg_Bue_1993", "SAM_Arg_Cor_1993",
"SAM_Arg_Ent_1993", "SAM_Arg_San_1993", "SAM_Bol_San_2001",
"SAM_Bra_Per_1993", "SAM_Bra_Sao_2001", "SAM_Bra_Bah_NA",
"SAM_Bra_Esp_NA", "SAM_Bra_Goi_1996", "SAM_Bra_Mar_NA", "SAM_Bra_Mat_NA",
"SAM_Bra_Bah_1993", "SAM_Bra_Rio_NA", "SAM_Col_Ant_NA", "SAM_Ecu_Imb_1994",
"SAM_Ecu_Pec_1994", "SAM_Ecu_Tun_1994", "SAM_Ecu_Azu_1997",
"SAM_Par_Caa_2001", "SAM_Par_Par_2001", "SAM_Per_Piu_1994",
"SAM_Per_Can_1994", "SAM_Per_Lim_1994", "SAM_Per_Tac_1994",
"SAM_Ven_Ven_1992", "AUS_Aus_Per_1994", "AUS_Aus_Per_2011",
"AUS_Aus_Wes_2011", "AUS_Aus_Wes_2015", "AUS_Aus_Wes_2016"
)), x = c(0.971185465, 0.959957553, 0.975074464, 0.971185465,
0.942539513, 0.942539513, 0.959957553, 0.949675685, 0.975074464,
0.949675685, 0.96823382, 0.951444429, 0.914758187, 0.965733122,
0.939819285, 0.978268071, 0.968965936, 0.964925752, 0.943911656,
0.829393223, 0.804226197, 0.957180344, 0.949150505, 0.96733028,
0.880829749, 0.86648621, 0.884244327, 0.959141918, 0.949828392,
0.938221117, 0.955754452, 0.957863477, 0.91340748, 0.872044799,
0.902641888, 0.932961912, 0.933447048, 0.936548539, 0.953347082,
0.831265914, 0.767998051, 0.971399981, 0.965990399, 0.971301897,
0.961281417, 0.957878235, 0.943745515, 0.978540307, 0.963631678,
0.967427473, 0.951993961, 0.952982237, 0.97494466, 0.968191119,
0.956617658, 0.95845831, 0.962761419, 0.954156934, 0.889045916,
0.812232525, 0.990101188, 0.768605046), factors = list())
Cheers, Pablo
May want to use these directions to add images: How to add images to a Biostars post
Thanks! Included the image now.
Please provide example data
dput(combo).Thank you! I have provided a link to the combo object
Link is broken, it is better to put the date in this post, no external links. Edit your post with output of
dput(combo), if the data is too big, maybe trydput(head(combo)).