英文:
Creating Sankey or Alluvial plot and stopping the flow where the "next_node" and "next_x" value is "NA" in R
问题
I am trying to create a Sankey or Alluvial plot using the ggplot2 library in R to visualize the flow of nodes based on the provided CSV data. The data includes columns for 'x', 'node', 'next_x', and 'next_node'. I want to create a plot where the flow is determined by the 'node' and 'next_node' columns. Additionally, I want to exclude any flows where 'next_x' is "NA".
Here's a simplified version of the CSV data I'm working with:
x node next_x next_nodeHomo_sapiens SLC35A1 Mus_musculus SLC35A1Homo_sapiens RARS2 Mus_musculus RARS2Homo_sapiens ORC3 Mus_musculus ORC3Homo_sapiens AKIRIN2 Mus_musculus AKIRIN2Homo_sapiens SPACA1 Mus_musculus SPACA1Homo_sapiens CNR1 Mus_musculus CNR1Homo_sapiens RNGTT Mus_musculus RNGTTHomo_sapiens PNRC1 Mus_musculus PNRC1Homo_sapiens PM20D2 Mus_musculus PM20D2Homo_sapiens SRSF12 Mus_musculus SRSF12Homo_sapiens GABRR1 Mus_musculus GABRR1Mus_musculus GABRR1 Rattus_norvegicus GABRR1Mus_musculus PM20D2 Rattus_norvegicus PM20D2Mus_musculus SRSF12 Rattus_norvegicus SRSF12Mus_musculus PNRC1 Rattus_norvegicus PNRC1Mus_musculus RNGTT Rattus_norvegicus RNGTTMus_musculus CNR1 Rattus_norvegicus CNR1Mus_musculus SPACA1 Rattus_norvegicus SPACA1Mus_musculus AKIRIN2 Rattus_norvegicus AKIRIN2Mus_musculus ORC3 Rattus_norvegicus ORC3Mus_musculus RARS2 Rattus_norvegicus RARS2Mus_musculus SLC35A1 Rattus_norvegicus SLC35A1Rattus_norvegicus GABRR1 Canis_lupus_familiaris GABRR1...
I'm using the ggplot2 library to create the plot, and I've tried the following script:
library(ggplot2)pl <- ggplot(data, aes(x = x, node = node, next_node = next_node, next_x = next_x, fill = factor(node), label = node)) +geom_sankey(flow.alpha = 0.5,node.color = "black",show.legend = FALSE,na.rm = TRUE) +geom_sankey_label(size = 3, color = "black", fill="white", hjust = 0.5) +theme_bw() +theme(legend.position = "none") +theme(axis.title = element_blank(),axis.text.y = element_blank(),axis.ticks = element_blank(),panel.grid = element_blank()) +scale_fill_viridis_d(option = "inferno") +labs(title = "Sankey diagram using ggplot",fill = "Nodes")
However, when I run this script, I'm encountering the following warning messages:
Warning messages:1: There was 1 warning in `dplyr::mutate()`.ℹ In argument: `dplyr::across(c(x, next_x), ~as.numeric(.), .names = ("n_{.col}"))`.Caused by warning:! NAs introduced by coercion2: There was 1 warning in `dplyr::mutate()`.ℹ In argument: `dplyr::across(c(x, next_x), ~as.numeric(.), .names = ("n_{.col}"))`.Caused by warning:! NAs introduced by coercion3: There was 1 warning in `dplyr::mutate()`.ℹ In argument: `dplyr::across(c(x, next_x), ~as.numeric(.), .names = ("n_{.col}"))`.Caused by warning:! NAs introduced by coercion
I also get an incomplete plot.
I'm seeking guidance on how to address this issue and successfully create the desired Sankey or Alluvial plot using ggplot2. Specifically, I want to achieve the following:
- Create a plot where the flow is based on 'node
英文:
I am trying to create a Sankey or Alluvial plot using the ggplot2 library in R to visualize the flow of nodes based on the provided CSV data. The data includes columns for 'x', 'node', 'next_x', and 'next_node'. I want to create a plot where the flow is determined by the 'node' and 'next_node' columns. Additionally, I want to exclude any flows where 'next_x' is "NA".
Here's a simplified version of the CSV data I'm working with:
x node next_x next_nodeHomo_sapiens SLC35A1 Mus_musculus SLC35A1Homo_sapiens RARS2 Mus_musculus RARS2Homo_sapiens ORC3 Mus_musculus ORC3Homo_sapiens AKIRIN2 Mus_musculus AKIRIN2Homo_sapiens SPACA1 Mus_musculus SPACA1Homo_sapiens CNR1 Mus_musculus CNR1Homo_sapiens RNGTT Mus_musculus RNGTTHomo_sapiens PNRC1 Mus_musculus PNRC1Homo_sapiens PM20D2 Mus_musculus PM20D2Homo_sapiens SRSF12 Mus_musculus SRSF12Homo_sapiens GABRR1 Mus_musculus GABRR1Mus_musculus GABRR1 Rattus_norvegicus GABRR1Mus_musculus PM20D2 Rattus_norvegicus PM20D2Mus_musculus SRSF12 Rattus_norvegicus SRSF12Mus_musculus PNRC1 Rattus_norvegicus PNRC1Mus_musculus RNGTT Rattus_norvegicus RNGTTMus_musculus CNR1 Rattus_norvegicus CNR1Mus_musculus SPACA1 Rattus_norvegicus SPACA1Mus_musculus AKIRIN2 Rattus_norvegicus AKIRIN2Mus_musculus ORC3 Rattus_norvegicus ORC3Mus_musculus RARS2 Rattus_norvegicus RARS2Mus_musculus SLC35A1 Rattus_norvegicus SLC35A1Rattus_norvegicus GABRR1 Canis_lupus_familiaris GABRR1Rattus_norvegicus PM20D2 Canis_lupus_familiaris PM20D2Rattus_norvegicus SRSF12 Canis_lupus_familiaris SRSF12Rattus_norvegicus PNRC1 Canis_lupus_familiaris PNRC1Rattus_norvegicus RNGTT Canis_lupus_familiaris RNGTTRattus_norvegicus CNR1 Canis_lupus_familiaris CNR1Rattus_norvegicus SPACA1 Canis_lupus_familiaris SPACA1Rattus_norvegicus AKIRIN2 Canis_lupus_familiaris AKIRIN2Rattus_norvegicus ORC3 Canis_lupus_familiaris ORC3Rattus_norvegicus RARS2 Canis_lupus_familiaris RARS2Rattus_norvegicus SLC35A1 Canis_lupus_familiaris SLC35A1Canis_lupus_familiaris SLC35A1 Monodelphis_domestica SLC35A1Canis_lupus_familiaris RARS2 Monodelphis_domestica RARS2Canis_lupus_familiaris ORC3 Monodelphis_domestica ORC3Canis_lupus_familiaris AKIRIN2 Monodelphis_domestica AKIRIN2Canis_lupus_familiaris SPACA1 Monodelphis_domestica SPACA1Canis_lupus_familiaris CNR1 Monodelphis_domestica CNR1Canis_lupus_familiaris RNGTT Monodelphis_domestica RNGTTCanis_lupus_familiaris PNRC1 Monodelphis_domestica PNRC1Canis_lupus_familiaris SRSF12 Monodelphis_domestica SRSF12Canis_lupus_familiaris PM20D2 Monodelphis_domestica PM20D2Canis_lupus_familiaris GABRR1 Monodelphis_domestica GABRR1Monodelphis_domestica SLC35A1 Ornithorhynchus_anatinus SLC35A1Monodelphis_domestica RARS2 Ornithorhynchus_anatinus RARS2Monodelphis_domestica ORC3 Ornithorhynchus_anatinus ORC3Monodelphis_domestica AKIRIN2 Ornithorhynchus_anatinus AKIRIN2Monodelphis_domestica SPACA1 Ornithorhynchus_anatinus SPACA1Monodelphis_domestica CNR1 Ornithorhynchus_anatinus CNR1Monodelphis_domestica RNGTT Ornithorhynchus_anatinus RNGTTMonodelphis_domestica PNRC1 Ornithorhynchus_anatinus PNRC1Monodelphis_domestica SRSF12 NA NAMonodelphis_domestica PM20D2 Ornithorhynchus_anatinus PM20D2Monodelphis_domestica GABRR1 NA NAOrnithorhynchus_anatinus SLC35A1 Gallus_gallus SLC35A1Ornithorhynchus_anatinus RARS2 Gallus_gallus RARS2Ornithorhynchus_anatinus ORC3 Gallus_gallus ORC3Ornithorhynchus_anatinus AKIRIN2 Gallus_gallus AKIRIN2Ornithorhynchus_anatinus SPACA1 Gallus_gallus SPACA1Ornithorhynchus_anatinus CNR1 Gallus_gallus CNR1Ornithorhynchus_anatinus RNGTT Gallus_gallus RNGTTOrnithorhynchus_anatinus PNRC1 Gallus_gallus PNRC1Ornithorhynchus_anatinus PM20D2 Gallus_gallus PM20D2Ornithorhynchus_anatinus LOC100076186 NA NAOrnithorhynchus_anatinus LOC114805750 NA NAGallus_gallus PM20D2 Taeniopygia_guttata PM20D2Gallus_gallus PNRC1 Taeniopygia_guttata PNRC1Gallus_gallus BORCS6 Taeniopygia_guttata BORCS6Gallus_gallus RNGTT Taeniopygia_guttata RNGTTGallus_gallus LOC101749895 NA NAGallus_gallus CNR1 Taeniopygia_guttata CNR1Gallus_gallus SPACA1 NA NAGallus_gallus AKIRIN2 Taeniopygia_guttata AKIRIN2Gallus_gallus ORC3 Taeniopygia_guttata ORC3Gallus_gallus RARS2 Taeniopygia_guttata RARS2Gallus_gallus SLC35A1 Taeniopygia_guttata SLC35A1Taeniopygia_guttata CFAP206 NA NATaeniopygia_guttata SLC35A1 Chelonia_mydas SLC35A1Taeniopygia_guttata RARS2 Chelonia_mydas RARS2Taeniopygia_guttata ORC3 Chelonia_mydas ORC3Taeniopygia_guttata AKIRIN2 Chelonia_mydas AKIRIN2Taeniopygia_guttata CNR1 Chelonia_mydas CNR1Taeniopygia_guttata RNGTT Chelonia_mydas RNGTTTaeniopygia_guttata BORCS6 NA NATaeniopygia_guttata PNRC1 Chelonia_mydas PNRC1Taeniopygia_guttata PM20D2 Chelonia_mydas PM20D2Taeniopygia_guttata GABRR1 Chelonia_mydas GABRR1Chelonia_mydas SLC35A1 Anolis_carolinensis SLC35A1Chelonia_mydas RARS2 Anolis_carolinensis RARS2Chelonia_mydas ORC3 Anolis_carolinensis ORC3Chelonia_mydas AKIRIN2 Anolis_carolinensis AKIRIN2Chelonia_mydas SPACA1 Anolis_carolinensis SPACA1Chelonia_mydas CNR1 Anolis_carolinensis CNR1Chelonia_mydas RNGTT Anolis_carolinensis RNGTTChelonia_mydas LOC102938330 NA NAChelonia_mydas PNRC1 Anolis_carolinensis PNRC1Chelonia_mydas PM20D2 Anolis_carolinensis PM20D2Chelonia_mydas GABRR1 NA NAAnolis_carolinensis PM20D2 NA NAAnolis_carolinensis SRSF12 NA NAAnolis_carolinensis PNRC1 NA NAAnolis_carolinensis RNGTT NA NAAnolis_carolinensis LOC107982676 NA NAAnolis_carolinensis CNR1 NA NAAnolis_carolinensis SPACA1 NA NAAnolis_carolinensis AKIRIN2 NA NAAnolis_carolinensis ORC3 NA NAAnolis_carolinensis RARS2 NA NAAnolis_carolinensis SLC35A1 NA NAXenopus_laevis GABRR2.S NA NAXenopus_laevis GABRR1.S NA NAXenopus_laevis PM20D2.S NA NAXenopus_laevis LOC108717975 NA NAXenopus_laevis RNGTT.S NA NAXenopus_laevis CNR1.S NA NAXenopus_laevis AKIRIN2.S NA NAXenopus_laevis ORC3.S NA NAXenopus_laevis RARS2.S NA NAXenopus_laevis SLC35A1.S NA NAXenopus_laevis LOC108717977 NA NALatimeria_chalumnae DDX24 NA NALatimeria_chalumnae PPP4R4 NA NALatimeria_chalumnae SERPINA10B NA NALatimeria_chalumnae ARRDC3A NA NALatimeria_chalumnae LOC102360869 NA NALatimeria_chalumnae CNR1 Protopterus_annectens CNR1Latimeria_chalumnae SPACA1 NA NALatimeria_chalumnae AKIRIN2 NA NALatimeria_chalumnae ORC3 NA NALatimeria_chalumnae RARS2 NA NALatimeria_chalumnae LOC102362557 NA NAProtopterus_annectens LOC122794922 NA NAProtopterus_annectens LOC122794923 NA NAProtopterus_annectens LOC122794924 NA NAProtopterus_annectens FBXL5 NA NAProtopterus_annectens CC2D2A NA NAProtopterus_annectens CNR1 Danio_rerio CNR1Protopterus_annectens CPEB2 NA NAProtopterus_annectens BOD1L1 NA NAProtopterus_annectens C1QTNF7 NA NAProtopterus_annectens NKX3-2 NA NAProtopterus_annectens RAB28 NA NADanio_rerio MYO6A NA NADanio_rerio LOC569340 NA NADanio_rerio MEI4 NA NADanio_rerio NT5E NA NADanio_rerio SNX14 NA NADanio_rerio CNR1 Oreochromis_niloticus CNR1Danio_rerio RNGTT Oreochromis_niloticus RNGTTDanio_rerio PNRC1 NA NADanio_rerio GABRR1 NA NADanio_rerio GABRR2B NA NADanio_rerio UBE2J1 NA NAOreochromis_niloticus SI:DKEY-174M14.3 NA NAOreochromis_niloticus RDH14B NA NAOreochromis_niloticus LOC102078481 NA NAOreochromis_niloticus RNGTT Scyliorhinus_canicula RNGTTOreochromis_niloticus LOC112842425 NA NAOreochromis_niloticus CNR1 Scyliorhinus_canicula CNR1Oreochromis_niloticus AKIRIN2 Scyliorhinus_canicula AKIRIN2Oreochromis_niloticus RARS2 Scyliorhinus_canicula RARS2Oreochromis_niloticus SLC35A1 Scyliorhinus_canicula SLC35A1Oreochromis_niloticus LOC100692709 NA NAOreochromis_niloticus LOC102081816 NA NAScyliorhinus_canicula SLC35A1 Petromyzon_marinus SLC35A1Scyliorhinus_canicula RARS2 Petromyzon_marinus RARS2Scyliorhinus_canicula ORC3 Petromyzon_marinus ORC3Scyliorhinus_canicula AKIRIN2 Petromyzon_marinus AKIRIN2Scyliorhinus_canicula LOC119967921 NA NAScyliorhinus_canicula CNR1 Petromyzon_marinus CNR1Scyliorhinus_canicula RNGTT Petromyzon_marinus RNGTTScyliorhinus_canicula LOC119967175 NA NAScyliorhinus_canicula PNRC1 NA NAScyliorhinus_canicula LOC119967178 NA NAScyliorhinus_canicula LOC119967180 NA NAPetromyzon_marinus LOC116953416 NA NAPetromyzon_marinus LOC116953419 NA NAPetromyzon_marinus CEP162 NA NAPetromyzon_marinus FBXL22 NA NAPetromyzon_marinus RNGTT NA NAPetromyzon_marinus CNR1 NA NAPetromyzon_marinus AKIRIN2 NA NAPetromyzon_marinus ORC3 NA NAPetromyzon_marinus RARS2 NA NAPetromyzon_marinus SLC35A1 NA NAPetromyzon_marinus RHBDL2 NA NA
I'm using the ggplot2 library to create the plot, and I've tried the following script:
library(ggplot2)pl <- ggplot(data, aes(x = x, node = node, next_node = next_node, next_x = next_x, fill = factor(node), label = node)) +geom_sankey(flow.alpha = 0.5,node.color = "black",show.legend = FALSE,na.rm = TRUE) +geom_sankey_label(size = 3, color = "black", fill="white", hjust = 0.5) +theme_bw() +theme(legend.position = "none") +theme(axis.title = element_blank(),axis.text.y = element_blank(),axis.ticks = element_blank(),panel.grid = element_blank()) +scale_fill_viridis_d(option = "inferno") +labs(title = "Sankey diagram using ggplot",fill = "Nodes")
However, when I run this script, I'm encountering the following warning messages:
Warning messages:1: There was 1 warning in `dplyr::mutate()`.ℹ In argument: `dplyr::across(c(x, next_x), ~as.numeric(.), .names = ("n_{.col}"))`.Caused by warning:! NAs introduced by coercion2: There was 1 warning in `dplyr::mutate()`.ℹ In argument: `dplyr::across(c(x, next_x), ~as.numeric(.), .names = ("n_{.col}"))`.Caused by warning:! NAs introduced by coercion3: There was 1 warning in `dplyr::mutate()`.ℹ In argument: `dplyr::across(c(x, next_x), ~as.numeric(.), .names = ("n_{.col}"))`.Caused by warning:! NAs introduced by coercion
I also get an incomplete plot:
Incomplete Sankey plot without flow
I'm seeking guidance on how to address this issue and successfully create the desired Sankey or Alluvial plot using ggplot2. Specifically, I want to achieve the following:
- Create a plot where the flow is based on 'node' and 'next_node'.
- Exclude flows where 'next_x' is "NA".
- Avoid the warning messages related to dplyr::mutate() and NAs.
Any assistance or insights into solving this problem would be greatly appreciated. Thank you in advance!
Edit:
This is my raw dataset of gene neighbors:
species gene start stop orientationHomo_sapiens SLC35A1 1 2 1Homo_sapiens RARS2 2 3 -1Homo_sapiens ORC3 3 4 1Homo_sapiens AKIRIN2 4 5 -1Homo_sapiens SPACA1 5 6 1Homo_sapiens CNR1 6 7 -1Homo_sapiens RNGTT 7 8 -1Homo_sapiens PNRC1 8 9 1Homo_sapiens PM20D2 9 10 1Homo_sapiens SRSF12 10 11 -1Homo_sapiens GABRR1 11 12 -1Mus_musculus GABRR1 1 2 1Mus_musculus PM20D2 2 3 -1Mus_musculus SRSF12 3 4 1Mus_musculus PNRC1 4 5 -1Mus_musculus RNGTT 5 6 1Mus_musculus CNR1 6 7 1Mus_musculus SPACA1 7 8 -1Mus_musculus AKIRIN2 8 9 1Mus_musculus ORC3 9 10 -1Mus_musculus RARS2 10 11 1Mus_musculus SLC35A1 11 12 -1Rattus_norvegicus GABRR1 1 2 1Rattus_norvegicus PM20D2 2 3 -1Rattus_norvegicus SRSF12 3 4 1Rattus_norvegicus PNRC1 4 5 -1Rattus_norvegicus RNGTT 5 6 1Rattus_norvegicus CNR1 6 7 1Rattus_norvegicus SPACA1 7 8 -1Rattus_norvegicus AKIRIN2 8 9 1Rattus_norvegicus ORC3 9 10 -1Rattus_norvegicus RARS2 10 11 1Rattus_norvegicus SLC35A1 11 12 -1Canis_lupus_familiaris SLC35A1 1 2 1Canis_lupus_familiaris RARS2 2 3 -1Canis_lupus_familiaris ORC3 3 4 1Canis_lupus_familiaris AKIRIN2 4 5 -1Canis_lupus_familiaris SPACA1 5 6 1Canis_lupus_familiaris CNR1 6 7 -1Canis_lupus_familiaris RNGTT 7 8 -1Canis_lupus_familiaris PNRC1 8 9 1Canis_lupus_familiaris SRSF12 9 10 -1Canis_lupus_familiaris PM20D2 10 11 1Canis_lupus_familiaris GABRR1 11 12 -1Monodelphis_domestica SLC35A1 1 2 1Monodelphis_domestica RARS2 2 3 -1Monodelphis_domestica ORC3 3 4 1Monodelphis_domestica AKIRIN2 4 5 -1Monodelphis_domestica SPACA1 5 6 1Monodelphis_domestica CNR1 6 7 -1Monodelphis_domestica RNGTT 7 8 -1Monodelphis_domestica PNRC1 8 9 1Monodelphis_domestica SRSF12 9 10 -1Monodelphis_domestica PM20D2 10 11 1Monodelphis_domestica GABRR1 11 12 -1Ornithorhynchus_anatinus SLC35A1 1 2 1Ornithorhynchus_anatinus RARS2 2 3 -1Ornithorhynchus_anatinus ORC3 3 4 1Ornithorhynchus_anatinus AKIRIN2 4 5 -1Ornithorhynchus_anatinus SPACA1 5 6 1Ornithorhynchus_anatinus CNR1 6 7 -1Ornithorhynchus_anatinus RNGTT 7 8 -1Ornithorhynchus_anatinus PNRC1 8 9 1Ornithorhynchus_anatinus PM20D2 9 10 1Ornithorhynchus_anatinus LOC100076186 10 11 -1Ornithorhynchus_anatinus LOC114805750 11 12 1Gallus_gallus PM20D2 1 2 -1Gallus_gallus PNRC1 2 3 -1Gallus_gallus BORCS6 3 4 1Gallus_gallus RNGTT 4 5 1Gallus_gallus LOC101749895 5 6 1Gallus_gallus CNR1 6 7 1Gallus_gallus SPACA1 7 8 -1Gallus_gallus AKIRIN2 8 9 1Gallus_gallus ORC3 9 10 -1Gallus_gallus RARS2 10 11 1Gallus_gallus SLC35A1 11 12 -1Taeniopygia_guttata CFAP206 1 2 1Taeniopygia_guttata SLC35A1 2 3 1Taeniopygia_guttata RARS2 3 4 -1Taeniopygia_guttata ORC3 4 5 1Taeniopygia_guttata AKIRIN2 5 6 -1Taeniopygia_guttata CNR1 6 7 -1Taeniopygia_guttata RNGTT 7 8 -1Taeniopygia_guttata BORCS6 8 9 -1Taeniopygia_guttata PNRC1 9 10 1Taeniopygia_guttata PM20D2 10 11 1Taeniopygia_guttata GABRR1 11 12 -1Chelonia_mydas SLC35A1 1 2 1Chelonia_mydas RARS2 2 3 -1Chelonia_mydas ORC3 3 4 1Chelonia_mydas AKIRIN2 4 5 -1Chelonia_mydas SPACA1 5 6 1Chelonia_mydas CNR1 6 7 -1Chelonia_mydas RNGTT 7 8 -1Chelonia_mydas LOC102938330 8 9 -1Chelonia_mydas PNRC1 9 10 1Chelonia_mydas PM20D2 10 11 1Chelonia_mydas GABRR1 11 12 -1Anolis_carolinensis PM20D2 1 2 -1Anolis_carolinensis SRSF12 2 3 1Anolis_carolinensis PNRC1 3 4 -1Anolis_carolinensis RNGTT 4 5 1Anolis_carolinensis LOC107982676 5 6 -1Anolis_carolinensis CNR1 6 7 1Anolis_carolinensis SPACA1 7 8 -1Anolis_carolinensis AKIRIN2 8 9 1Anolis_carolinensis ORC3 9 10 -1Anolis_carolinensis RARS2 10 11 1Anolis_carolinensis SLC35A1 11 12 -1Xenopus_laevis GABRR2.S 1 2 1Xenopus_laevis GABRR1.S 2 3 1Xenopus_laevis PM20D2.S 3 4 -1Xenopus_laevis LOC108717975 4 5 1Xenopus_laevis RNGTT.S 5 6 1Xenopus_laevis CNR1.S 6 7 1Xenopus_laevis AKIRIN2.S 7 8 1Xenopus_laevis ORC3.S 8 9 -1Xenopus_laevis RARS2.S 9 10 1Xenopus_laevis SLC35A1.S 10 11 -1Xenopus_laevis LOC108717977 11 12 1Latimeria_chalumnae DDX24 1 2 -1Latimeria_chalumnae PPP4R4 2 3 1Latimeria_chalumnae SERPINA10B 3 4 -1Latimeria_chalumnae ARRDC3A 4 5 1Latimeria_chalumnae LOC102360869 5 6 -1Latimeria_chalumnae CNR1 6 7 1Latimeria_chalumnae SPACA1 7 8 -1Latimeria_chalumnae AKIRIN2 8 9 1Latimeria_chalumnae ORC3 9 10 -1Latimeria_chalumnae RARS2 10 11 1Latimeria_chalumnae LOC102362557 11 12 1Protopterus_annectens LOC122794922 1 2 1Protopterus_annectens LOC122794923 2 3 1Protopterus_annectens LOC122794924 3 4 1Protopterus_annectens FBXL5 4 5 1Protopterus_annectens CC2D2A 5 6 -1Protopterus_annectens CNR1 6 7 1Protopterus_annectens CPEB2 7 8 -1Protopterus_annectens BOD1L1 8 9 -1Protopterus_annectens C1QTNF7 9 10 -1Protopterus_annectens NKX3-2 10 11 1Protopterus_annectens RAB28 11 12 1Danio_rerio MYO6A 1 2 1Danio_rerio LOC569340 2 3 -1Danio_rerio MEI4 3 4 1Danio_rerio NT5E 4 5 1Danio_rerio SNX14 5 6 -1Danio_rerio CNR1 6 7 -1Danio_rerio RNGTT 7 8 -1Danio_rerio PNRC1 8 9 1Danio_rerio GABRR1 9 10 -1Danio_rerio GABRR2B 10 11 -1Danio_rerio UBE2J1 11 12 -1Oreochromis_niloticus SI:DKEY-174M14.3 1 2 1Oreochromis_niloticus RDH14B 2 3 -1Oreochromis_niloticus LOC102078481 3 4 1Oreochromis_niloticus RNGTT 4 5 1Oreochromis_niloticus LOC112842425 5 6 -1Oreochromis_niloticus CNR1 6 7 1Oreochromis_niloticus AKIRIN2 7 8 1Oreochromis_niloticus RARS2 8 9 1Oreochromis_niloticus SLC35A1 9 10 -1Oreochromis_niloticus LOC100692709 10 11 -1Oreochromis_niloticus LOC102081816 11 12 1Scyliorhinus_canicula SLC35A1 1 2 1Scyliorhinus_canicula RARS2 2 3 -1Scyliorhinus_canicula ORC3 3 4 1Scyliorhinus_canicula AKIRIN2 4 5 -1Scyliorhinus_canicula LOC119967921 5 6 1Scyliorhinus_canicula CNR1 6 7 -1Scyliorhinus_canicula RNGTT 7 8 -1Scyliorhinus_canicula LOC119967175 8 9 -1Scyliorhinus_canicula PNRC1 9 10 1Scyliorhinus_canicula LOC119967178 10 11 1Scyliorhinus_canicula LOC119967180 11 12 -1Petromyzon_marinus LOC116953416 1 2 -1Petromyzon_marinus LOC116953419 2 3 -1Petromyzon_marinus CEP162 3 4 1Petromyzon_marinus FBXL22 4 5 -1Petromyzon_marinus RNGTT 5 6 1Petromyzon_marinus CNR1 6 7 1Petromyzon_marinus AKIRIN2 7 8 1Petromyzon_marinus ORC3 8 9 -1Petromyzon_marinus RARS2 9 10 1Petromyzon_marinus SLC35A1 10 11 -1Petromyzon_marinus RHBDL2 11 12 1
Edit 2:
I've managed to get few flows connected but it is still incorrect. The problem is probably with the order of the rows. Can somebody please suggest something?
答案1
得分: 1
这里不清楚为什么你要尝试绘制桑基图。每个连接只有单一的流动，如果你将所有基因都绘制在同一高度，那么所有连接都是水平的。将其绘制成图表更有意义且更整洁：
library(tidyverse)library(tidygraph)library(ggraph)data.frame(from = paste(data[[1]], data[[2]]),to = paste(data[[3]], data[[4]])) %>%filter(to != "NA NA") %>%as_tbl_graph() %>%mutate(Species = str_replace(str_remove(name, " .*"), "_", "\n"),Gene = str_remove(name, ".* "),ypos = as.numeric(factor(Gene)),xpos = as.numeric(factor(Species, unique(Species)))) %>%ggraph(layout = "manual", x = xpos, y = ypos) +geom_edge_fan(width = 4, alpha = 0.2) +geom_node_point(aes(fill = Gene), shape = 22, size = 12) +geom_node_label(aes(label = Gene), size = 2.5) +geom_text(aes(x = xpos, label = Species, y = 0), check_overlap = TRUE) +scale_fill_viridis_d(guide = "none") +scale_edge_color_viridis(guide = "none") +theme_void()
你甚至可以将其绘制成点线图：
library(tidyverse)levs <- names(sort(table(c(data$node, data$next_node))))data %>%mutate(x = gsub("_", "\n", x), next_x = gsub("_", "\n", next_x)) %>%mutate(node = factor(node, levs),next_node = factor(next_node, levs)) %>%ggplot(aes(x, node, color = node)) +geom_segment(aes(xend = next_x, yend = next_node), linewidth = 1) +geom_point(size = 2.5) +geom_point(aes(x = next_x, y = next_node), size = 2.5) +scale_color_viridis_d(guide = "none") +scale_y_discrete(limits = levs) +theme_minimal()
英文:
It's not clear why you are trying to draw a Sankey diagram here. Each connection only has a single flow, and if you draw all the genes at the same height, all the connections are horizontal. It makes more sense and is tidier as a graph:
library(tidyverse)library(tidygraph)library(ggraph)data.frame(from = paste(data[[1]], data[[2]]),to = paste(data[[3]], data[[4]])) %>%filter(to != "NA NA") %>%as_tbl_graph() %>%mutate(Species = str_replace(str_remove(name, " .*"), "_", "\n"),Gene = str_remove(name, ".* "),ypos = as.numeric(factor(Gene)),xpos = as.numeric(factor(Species, unique(Species)))) %>%ggraph(layout = "manual", x = xpos, y = ypos) +geom_edge_fan(width = 4, alpha = 0.2) +geom_node_point(aes(fill = Gene), shape = 22, size = 12) +geom_node_label(aes(label = Gene), size = 2.5) +geom_text(aes(x = xpos, label = Species, y = 0), check_overlap = TRUE) +scale_fill_viridis_d(guide = "none") +scale_edge_color_viridis(guide = "none") +theme_void()
You could even just do it as a dot-and-line plot:
library(tidyverse)levs <- names(sort(table(c(data$node, data$next_node))))data %>%mutate(x = gsub("_", "\n", x), next_x = gsub("_", "\n", next_x)) %>%mutate(node = factor(node, levs),next_node = factor(next_node, levs)) %>%ggplot(aes(x, node, color = node)) +geom_segment(aes(xend = next_x, yend = next_node), linewidth = 1) +geom_point(size = 2.5) +geom_point(aes(x = next_x, y = next_node), size = 2.5) +scale_color_viridis_d(guide = "none") +scale_y_discrete(limits = levs) +theme_minimal()
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