在R中创建Sankey或Alluvial图,并在”next_node”和”next_x”值为”NA”时停止流动。

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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_node
Homo_sapiens	SLC35A1	Mus_musculus	SLC35A1
Homo_sapiens	RARS2	Mus_musculus	RARS2
Homo_sapiens	ORC3	Mus_musculus	ORC3
Homo_sapiens	AKIRIN2	Mus_musculus	AKIRIN2
Homo_sapiens	SPACA1	Mus_musculus	SPACA1
Homo_sapiens	CNR1	Mus_musculus	CNR1
Homo_sapiens	RNGTT	Mus_musculus	RNGTT
Homo_sapiens	PNRC1	Mus_musculus	PNRC1
Homo_sapiens	PM20D2	Mus_musculus	PM20D2
Homo_sapiens	SRSF12	Mus_musculus	SRSF12
Homo_sapiens	GABRR1	Mus_musculus	GABRR1
Mus_musculus	GABRR1	Rattus_norvegicus	GABRR1
Mus_musculus	PM20D2	Rattus_norvegicus	PM20D2
Mus_musculus	SRSF12	Rattus_norvegicus	SRSF12
Mus_musculus	PNRC1	Rattus_norvegicus	PNRC1
Mus_musculus	RNGTT	Rattus_norvegicus	RNGTT
Mus_musculus	CNR1	Rattus_norvegicus	CNR1
Mus_musculus	SPACA1	Rattus_norvegicus	SPACA1
Mus_musculus	AKIRIN2	Rattus_norvegicus	AKIRIN2
Mus_musculus	ORC3	Rattus_norvegicus	ORC3
Mus_musculus	RARS2	Rattus_norvegicus	RARS2
Mus_musculus	SLC35A1	Rattus_norvegicus	SLC35A1
Rattus_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 coercion 
2: 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 
3: 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:

  1. 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_node
Homo_sapiens	SLC35A1	Mus_musculus	SLC35A1
Homo_sapiens	RARS2	Mus_musculus	RARS2
Homo_sapiens	ORC3	Mus_musculus	ORC3
Homo_sapiens	AKIRIN2	Mus_musculus	AKIRIN2
Homo_sapiens	SPACA1	Mus_musculus	SPACA1
Homo_sapiens	CNR1	Mus_musculus	CNR1
Homo_sapiens	RNGTT	Mus_musculus	RNGTT
Homo_sapiens	PNRC1	Mus_musculus	PNRC1
Homo_sapiens	PM20D2	Mus_musculus	PM20D2
Homo_sapiens	SRSF12	Mus_musculus	SRSF12
Homo_sapiens	GABRR1	Mus_musculus	GABRR1
Mus_musculus	GABRR1	Rattus_norvegicus	GABRR1
Mus_musculus	PM20D2	Rattus_norvegicus	PM20D2
Mus_musculus	SRSF12	Rattus_norvegicus	SRSF12
Mus_musculus	PNRC1	Rattus_norvegicus	PNRC1
Mus_musculus	RNGTT	Rattus_norvegicus	RNGTT
Mus_musculus	CNR1	Rattus_norvegicus	CNR1
Mus_musculus	SPACA1	Rattus_norvegicus	SPACA1
Mus_musculus	AKIRIN2	Rattus_norvegicus	AKIRIN2
Mus_musculus	ORC3	Rattus_norvegicus	ORC3
Mus_musculus	RARS2	Rattus_norvegicus	RARS2
Mus_musculus	SLC35A1	Rattus_norvegicus	SLC35A1
Rattus_norvegicus	GABRR1	Canis_lupus_familiaris	GABRR1
Rattus_norvegicus	PM20D2	Canis_lupus_familiaris	PM20D2
Rattus_norvegicus	SRSF12	Canis_lupus_familiaris	SRSF12
Rattus_norvegicus	PNRC1	Canis_lupus_familiaris	PNRC1
Rattus_norvegicus	RNGTT	Canis_lupus_familiaris	RNGTT
Rattus_norvegicus	CNR1	Canis_lupus_familiaris	CNR1
Rattus_norvegicus	SPACA1	Canis_lupus_familiaris	SPACA1
Rattus_norvegicus	AKIRIN2	Canis_lupus_familiaris	AKIRIN2
Rattus_norvegicus	ORC3	Canis_lupus_familiaris	ORC3
Rattus_norvegicus	RARS2	Canis_lupus_familiaris	RARS2
Rattus_norvegicus	SLC35A1	Canis_lupus_familiaris	SLC35A1
Canis_lupus_familiaris	SLC35A1	Monodelphis_domestica	SLC35A1
Canis_lupus_familiaris	RARS2	Monodelphis_domestica	RARS2
Canis_lupus_familiaris	ORC3	Monodelphis_domestica	ORC3
Canis_lupus_familiaris	AKIRIN2	Monodelphis_domestica	AKIRIN2
Canis_lupus_familiaris	SPACA1	Monodelphis_domestica	SPACA1
Canis_lupus_familiaris	CNR1	Monodelphis_domestica	CNR1
Canis_lupus_familiaris	RNGTT	Monodelphis_domestica	RNGTT
Canis_lupus_familiaris	PNRC1	Monodelphis_domestica	PNRC1
Canis_lupus_familiaris	SRSF12	Monodelphis_domestica	SRSF12
Canis_lupus_familiaris	PM20D2	Monodelphis_domestica	PM20D2
Canis_lupus_familiaris	GABRR1	Monodelphis_domestica	GABRR1
Monodelphis_domestica	SLC35A1	Ornithorhynchus_anatinus	SLC35A1
Monodelphis_domestica	RARS2	Ornithorhynchus_anatinus	RARS2
Monodelphis_domestica	ORC3	Ornithorhynchus_anatinus	ORC3
Monodelphis_domestica	AKIRIN2	Ornithorhynchus_anatinus	AKIRIN2
Monodelphis_domestica	SPACA1	Ornithorhynchus_anatinus	SPACA1
Monodelphis_domestica	CNR1	Ornithorhynchus_anatinus	CNR1
Monodelphis_domestica	RNGTT	Ornithorhynchus_anatinus	RNGTT
Monodelphis_domestica	PNRC1	Ornithorhynchus_anatinus	PNRC1
Monodelphis_domestica	SRSF12	NA	NA
Monodelphis_domestica	PM20D2	Ornithorhynchus_anatinus	PM20D2
Monodelphis_domestica	GABRR1	NA	NA
Ornithorhynchus_anatinus	SLC35A1	Gallus_gallus	SLC35A1
Ornithorhynchus_anatinus	RARS2	Gallus_gallus	RARS2
Ornithorhynchus_anatinus	ORC3	Gallus_gallus	ORC3
Ornithorhynchus_anatinus	AKIRIN2	Gallus_gallus	AKIRIN2
Ornithorhynchus_anatinus	SPACA1	Gallus_gallus	SPACA1
Ornithorhynchus_anatinus	CNR1	Gallus_gallus	CNR1
Ornithorhynchus_anatinus	RNGTT	Gallus_gallus	RNGTT
Ornithorhynchus_anatinus	PNRC1	Gallus_gallus	PNRC1
Ornithorhynchus_anatinus	PM20D2	Gallus_gallus	PM20D2
Ornithorhynchus_anatinus	LOC100076186	NA	NA
Ornithorhynchus_anatinus	LOC114805750	NA	NA
Gallus_gallus	PM20D2	Taeniopygia_guttata	PM20D2
Gallus_gallus	PNRC1	Taeniopygia_guttata	PNRC1
Gallus_gallus	BORCS6	Taeniopygia_guttata	BORCS6
Gallus_gallus	RNGTT	Taeniopygia_guttata	RNGTT
Gallus_gallus	LOC101749895	NA	NA
Gallus_gallus	CNR1	Taeniopygia_guttata	CNR1
Gallus_gallus	SPACA1	NA	NA
Gallus_gallus	AKIRIN2	Taeniopygia_guttata	AKIRIN2
Gallus_gallus	ORC3	Taeniopygia_guttata	ORC3
Gallus_gallus	RARS2	Taeniopygia_guttata	RARS2
Gallus_gallus	SLC35A1	Taeniopygia_guttata	SLC35A1
Taeniopygia_guttata	CFAP206	NA	NA
Taeniopygia_guttata	SLC35A1	Chelonia_mydas	SLC35A1
Taeniopygia_guttata	RARS2	Chelonia_mydas	RARS2
Taeniopygia_guttata	ORC3	Chelonia_mydas	ORC3
Taeniopygia_guttata	AKIRIN2	Chelonia_mydas	AKIRIN2
Taeniopygia_guttata	CNR1	Chelonia_mydas	CNR1
Taeniopygia_guttata	RNGTT	Chelonia_mydas	RNGTT
Taeniopygia_guttata	BORCS6	NA	NA
Taeniopygia_guttata	PNRC1	Chelonia_mydas	PNRC1
Taeniopygia_guttata	PM20D2	Chelonia_mydas	PM20D2
Taeniopygia_guttata	GABRR1	Chelonia_mydas	GABRR1
Chelonia_mydas	SLC35A1	Anolis_carolinensis	SLC35A1
Chelonia_mydas	RARS2	Anolis_carolinensis	RARS2
Chelonia_mydas	ORC3	Anolis_carolinensis	ORC3
Chelonia_mydas	AKIRIN2	Anolis_carolinensis	AKIRIN2
Chelonia_mydas	SPACA1	Anolis_carolinensis	SPACA1
Chelonia_mydas	CNR1	Anolis_carolinensis	CNR1
Chelonia_mydas	RNGTT	Anolis_carolinensis	RNGTT
Chelonia_mydas	LOC102938330	NA	NA
Chelonia_mydas	PNRC1	Anolis_carolinensis	PNRC1
Chelonia_mydas	PM20D2	Anolis_carolinensis	PM20D2
Chelonia_mydas	GABRR1	NA	NA
Anolis_carolinensis	PM20D2	NA	NA
Anolis_carolinensis	SRSF12	NA	NA
Anolis_carolinensis	PNRC1	NA	NA
Anolis_carolinensis	RNGTT	NA	NA
Anolis_carolinensis	LOC107982676	NA	NA
Anolis_carolinensis	CNR1	NA	NA
Anolis_carolinensis	SPACA1	NA	NA
Anolis_carolinensis	AKIRIN2	NA	NA
Anolis_carolinensis	ORC3	NA	NA
Anolis_carolinensis	RARS2	NA	NA
Anolis_carolinensis	SLC35A1	NA	NA
Xenopus_laevis	GABRR2.S	NA	NA
Xenopus_laevis	GABRR1.S	NA	NA
Xenopus_laevis	PM20D2.S	NA	NA
Xenopus_laevis	LOC108717975	NA	NA
Xenopus_laevis	RNGTT.S	NA	NA
Xenopus_laevis	CNR1.S	NA	NA
Xenopus_laevis	AKIRIN2.S	NA	NA
Xenopus_laevis	ORC3.S	NA	NA
Xenopus_laevis	RARS2.S	NA	NA
Xenopus_laevis	SLC35A1.S	NA	NA
Xenopus_laevis	LOC108717977	NA	NA
Latimeria_chalumnae	DDX24	NA	NA
Latimeria_chalumnae	PPP4R4	NA	NA
Latimeria_chalumnae	SERPINA10B	NA	NA
Latimeria_chalumnae	ARRDC3A	NA	NA
Latimeria_chalumnae	LOC102360869	NA	NA
Latimeria_chalumnae	CNR1	Protopterus_annectens	CNR1
Latimeria_chalumnae	SPACA1	NA	NA
Latimeria_chalumnae	AKIRIN2	NA	NA
Latimeria_chalumnae	ORC3	NA	NA
Latimeria_chalumnae	RARS2	NA	NA
Latimeria_chalumnae	LOC102362557	NA	NA
Protopterus_annectens	LOC122794922	NA	NA
Protopterus_annectens	LOC122794923	NA	NA
Protopterus_annectens	LOC122794924	NA	NA
Protopterus_annectens	FBXL5	NA	NA
Protopterus_annectens	CC2D2A	NA	NA
Protopterus_annectens	CNR1	Danio_rerio	CNR1
Protopterus_annectens	CPEB2	NA	NA
Protopterus_annectens	BOD1L1	NA	NA
Protopterus_annectens	C1QTNF7	NA	NA
Protopterus_annectens	NKX3-2	NA	NA
Protopterus_annectens	RAB28	NA	NA
Danio_rerio	MYO6A	NA	NA
Danio_rerio	LOC569340	NA	NA
Danio_rerio	MEI4	NA	NA
Danio_rerio	NT5E	NA	NA
Danio_rerio	SNX14	NA	NA
Danio_rerio	CNR1	Oreochromis_niloticus	CNR1
Danio_rerio	RNGTT	Oreochromis_niloticus	RNGTT
Danio_rerio	PNRC1	NA	NA
Danio_rerio	GABRR1	NA	NA
Danio_rerio	GABRR2B	NA	NA
Danio_rerio	UBE2J1	NA	NA
Oreochromis_niloticus	SI:DKEY-174M14.3	NA	NA
Oreochromis_niloticus	RDH14B	NA	NA
Oreochromis_niloticus	LOC102078481	NA	NA
Oreochromis_niloticus	RNGTT	Scyliorhinus_canicula	RNGTT
Oreochromis_niloticus	LOC112842425	NA	NA
Oreochromis_niloticus	CNR1	Scyliorhinus_canicula	CNR1
Oreochromis_niloticus	AKIRIN2	Scyliorhinus_canicula	AKIRIN2
Oreochromis_niloticus	RARS2	Scyliorhinus_canicula	RARS2
Oreochromis_niloticus	SLC35A1	Scyliorhinus_canicula	SLC35A1
Oreochromis_niloticus	LOC100692709	NA	NA
Oreochromis_niloticus	LOC102081816	NA	NA
Scyliorhinus_canicula	SLC35A1	Petromyzon_marinus	SLC35A1
Scyliorhinus_canicula	RARS2	Petromyzon_marinus	RARS2
Scyliorhinus_canicula	ORC3	Petromyzon_marinus	ORC3
Scyliorhinus_canicula	AKIRIN2	Petromyzon_marinus	AKIRIN2
Scyliorhinus_canicula	LOC119967921	NA	NA
Scyliorhinus_canicula	CNR1	Petromyzon_marinus	CNR1
Scyliorhinus_canicula	RNGTT	Petromyzon_marinus	RNGTT
Scyliorhinus_canicula	LOC119967175	NA	NA
Scyliorhinus_canicula	PNRC1	NA	NA
Scyliorhinus_canicula	LOC119967178	NA	NA
Scyliorhinus_canicula	LOC119967180	NA	NA
Petromyzon_marinus	LOC116953416	NA	NA
Petromyzon_marinus	LOC116953419	NA	NA
Petromyzon_marinus	CEP162	NA	NA
Petromyzon_marinus	FBXL22	NA	NA
Petromyzon_marinus	RNGTT	NA	NA
Petromyzon_marinus	CNR1	NA	NA
Petromyzon_marinus	AKIRIN2	NA	NA
Petromyzon_marinus	ORC3	NA	NA
Petromyzon_marinus	RARS2	NA	NA
Petromyzon_marinus	SLC35A1	NA	NA
Petromyzon_marinus	RHBDL2	NA	NA

I'm using the ggplot2 library to create the plot, and I've tried the following script:

library(ggplot2)
pl &lt;- 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 = &quot;black&quot;,
show.legend = FALSE,
na.rm = TRUE) +
geom_sankey_label(size = 3, color = &quot;black&quot;, fill=&quot;white&quot;, hjust = 0.5) +
theme_bw() +
theme(legend.position = &quot;none&quot;) +
theme(axis.title = element_blank(),
axis.text.y = element_blank(),
axis.ticks = element_blank(),
panel.grid = element_blank()) +
scale_fill_viridis_d(option = &quot;inferno&quot;) +
labs(title = &quot;Sankey diagram using ggplot&quot;,
fill = &quot;Nodes&quot;)

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 = (&quot;n_{.col}&quot;))`.
Caused by warning:
! NAs introduced by coercion 
2: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `dplyr::across(c(x, next_x), ~as.numeric(.), .names = (&quot;n_{.col}&quot;))`.
Caused by warning:
! NAs introduced by coercion 
3: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `dplyr::across(c(x, next_x), ~as.numeric(.), .names = (&quot;n_{.col}&quot;))`.
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:

  1. Create a plot where the flow is based on 'node' and 'next_node'.
  2. Exclude flows where 'next_x' is "NA".
  3. 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	orientation
Homo_sapiens	SLC35A1	1	2	1
Homo_sapiens	RARS2	2	3	-1
Homo_sapiens	ORC3	3	4	1
Homo_sapiens	AKIRIN2	4	5	-1
Homo_sapiens	SPACA1	5	6	1
Homo_sapiens	CNR1	6	7	-1
Homo_sapiens	RNGTT	7	8	-1
Homo_sapiens	PNRC1	8	9	1
Homo_sapiens	PM20D2	9	10	1
Homo_sapiens	SRSF12	10	11	-1
Homo_sapiens	GABRR1	11	12	-1
Mus_musculus	GABRR1	1	2	1
Mus_musculus	PM20D2	2	3	-1
Mus_musculus	SRSF12	3	4	1
Mus_musculus	PNRC1	4	5	-1
Mus_musculus	RNGTT	5	6	1
Mus_musculus	CNR1	6	7	1
Mus_musculus	SPACA1	7	8	-1
Mus_musculus	AKIRIN2	8	9	1
Mus_musculus	ORC3	9	10	-1
Mus_musculus	RARS2	10	11	1
Mus_musculus	SLC35A1	11	12	-1
Rattus_norvegicus	GABRR1	1	2	1
Rattus_norvegicus	PM20D2	2	3	-1
Rattus_norvegicus	SRSF12	3	4	1
Rattus_norvegicus	PNRC1	4	5	-1
Rattus_norvegicus	RNGTT	5	6	1
Rattus_norvegicus	CNR1	6	7	1
Rattus_norvegicus	SPACA1	7	8	-1
Rattus_norvegicus	AKIRIN2	8	9	1
Rattus_norvegicus	ORC3	9	10	-1
Rattus_norvegicus	RARS2	10	11	1
Rattus_norvegicus	SLC35A1	11	12	-1
Canis_lupus_familiaris	SLC35A1	1	2	1
Canis_lupus_familiaris	RARS2	2	3	-1
Canis_lupus_familiaris	ORC3	3	4	1
Canis_lupus_familiaris	AKIRIN2	4	5	-1
Canis_lupus_familiaris	SPACA1	5	6	1
Canis_lupus_familiaris	CNR1	6	7	-1
Canis_lupus_familiaris	RNGTT	7	8	-1
Canis_lupus_familiaris	PNRC1	8	9	1
Canis_lupus_familiaris	SRSF12	9	10	-1
Canis_lupus_familiaris	PM20D2	10	11	1
Canis_lupus_familiaris	GABRR1	11	12	-1
Monodelphis_domestica	SLC35A1	1	2	1
Monodelphis_domestica	RARS2	2	3	-1
Monodelphis_domestica	ORC3	3	4	1
Monodelphis_domestica	AKIRIN2	4	5	-1
Monodelphis_domestica	SPACA1	5	6	1
Monodelphis_domestica	CNR1	6	7	-1
Monodelphis_domestica	RNGTT	7	8	-1
Monodelphis_domestica	PNRC1	8	9	1
Monodelphis_domestica	SRSF12	9	10	-1
Monodelphis_domestica	PM20D2	10	11	1
Monodelphis_domestica	GABRR1	11	12	-1
Ornithorhynchus_anatinus	SLC35A1	1	2	1
Ornithorhynchus_anatinus	RARS2	2	3	-1
Ornithorhynchus_anatinus	ORC3	3	4	1
Ornithorhynchus_anatinus	AKIRIN2	4	5	-1
Ornithorhynchus_anatinus	SPACA1	5	6	1
Ornithorhynchus_anatinus	CNR1	6	7	-1
Ornithorhynchus_anatinus	RNGTT	7	8	-1
Ornithorhynchus_anatinus	PNRC1	8	9	1
Ornithorhynchus_anatinus	PM20D2	9	10	1
Ornithorhynchus_anatinus	LOC100076186	10	11	-1
Ornithorhynchus_anatinus	LOC114805750	11	12	1
Gallus_gallus	PM20D2	1	2	-1
Gallus_gallus	PNRC1	2	3	-1
Gallus_gallus	BORCS6	3	4	1
Gallus_gallus	RNGTT	4	5	1
Gallus_gallus	LOC101749895	5	6	1
Gallus_gallus	CNR1	6	7	1
Gallus_gallus	SPACA1	7	8	-1
Gallus_gallus	AKIRIN2	8	9	1
Gallus_gallus	ORC3	9	10	-1
Gallus_gallus	RARS2	10	11	1
Gallus_gallus	SLC35A1	11	12	-1
Taeniopygia_guttata	CFAP206	1	2	1
Taeniopygia_guttata	SLC35A1	2	3	1
Taeniopygia_guttata	RARS2	3	4	-1
Taeniopygia_guttata	ORC3	4	5	1
Taeniopygia_guttata	AKIRIN2	5	6	-1
Taeniopygia_guttata	CNR1	6	7	-1
Taeniopygia_guttata	RNGTT	7	8	-1
Taeniopygia_guttata	BORCS6	8	9	-1
Taeniopygia_guttata	PNRC1	9	10	1
Taeniopygia_guttata	PM20D2	10	11	1
Taeniopygia_guttata	GABRR1	11	12	-1
Chelonia_mydas	SLC35A1	1	2	1
Chelonia_mydas	RARS2	2	3	-1
Chelonia_mydas	ORC3	3	4	1
Chelonia_mydas	AKIRIN2	4	5	-1
Chelonia_mydas	SPACA1	5	6	1
Chelonia_mydas	CNR1	6	7	-1
Chelonia_mydas	RNGTT	7	8	-1
Chelonia_mydas	LOC102938330	8	9	-1
Chelonia_mydas	PNRC1	9	10	1
Chelonia_mydas	PM20D2	10	11	1
Chelonia_mydas	GABRR1	11	12	-1
Anolis_carolinensis	PM20D2	1	2	-1
Anolis_carolinensis	SRSF12	2	3	1
Anolis_carolinensis	PNRC1	3	4	-1
Anolis_carolinensis	RNGTT	4	5	1
Anolis_carolinensis	LOC107982676	5	6	-1
Anolis_carolinensis	CNR1	6	7	1
Anolis_carolinensis	SPACA1	7	8	-1
Anolis_carolinensis	AKIRIN2	8	9	1
Anolis_carolinensis	ORC3	9	10	-1
Anolis_carolinensis	RARS2	10	11	1
Anolis_carolinensis	SLC35A1	11	12	-1
Xenopus_laevis	GABRR2.S	1	2	1
Xenopus_laevis	GABRR1.S	2	3	1
Xenopus_laevis	PM20D2.S	3	4	-1
Xenopus_laevis	LOC108717975	4	5	1
Xenopus_laevis	RNGTT.S	5	6	1
Xenopus_laevis	CNR1.S	6	7	1
Xenopus_laevis	AKIRIN2.S	7	8	1
Xenopus_laevis	ORC3.S	8	9	-1
Xenopus_laevis	RARS2.S	9	10	1
Xenopus_laevis	SLC35A1.S	10	11	-1
Xenopus_laevis	LOC108717977	11	12	1
Latimeria_chalumnae	DDX24	1	2	-1
Latimeria_chalumnae	PPP4R4	2	3	1
Latimeria_chalumnae	SERPINA10B	3	4	-1
Latimeria_chalumnae	ARRDC3A	4	5	1
Latimeria_chalumnae	LOC102360869	5	6	-1
Latimeria_chalumnae	CNR1	6	7	1
Latimeria_chalumnae	SPACA1	7	8	-1
Latimeria_chalumnae	AKIRIN2	8	9	1
Latimeria_chalumnae	ORC3	9	10	-1
Latimeria_chalumnae	RARS2	10	11	1
Latimeria_chalumnae	LOC102362557	11	12	1
Protopterus_annectens	LOC122794922	1	2	1
Protopterus_annectens	LOC122794923	2	3	1
Protopterus_annectens	LOC122794924	3	4	1
Protopterus_annectens	FBXL5	4	5	1
Protopterus_annectens	CC2D2A	5	6	-1
Protopterus_annectens	CNR1	6	7	1
Protopterus_annectens	CPEB2	7	8	-1
Protopterus_annectens	BOD1L1	8	9	-1
Protopterus_annectens	C1QTNF7	9	10	-1
Protopterus_annectens	NKX3-2	10	11	1
Protopterus_annectens	RAB28	11	12	1
Danio_rerio	MYO6A	1	2	1
Danio_rerio	LOC569340	2	3	-1
Danio_rerio	MEI4	3	4	1
Danio_rerio	NT5E	4	5	1
Danio_rerio	SNX14	5	6	-1
Danio_rerio	CNR1	6	7	-1
Danio_rerio	RNGTT	7	8	-1
Danio_rerio	PNRC1	8	9	1
Danio_rerio	GABRR1	9	10	-1
Danio_rerio	GABRR2B	10	11	-1
Danio_rerio	UBE2J1	11	12	-1
Oreochromis_niloticus	SI:DKEY-174M14.3	1	2	1
Oreochromis_niloticus	RDH14B	2	3	-1
Oreochromis_niloticus	LOC102078481	3	4	1
Oreochromis_niloticus	RNGTT	4	5	1
Oreochromis_niloticus	LOC112842425	5	6	-1
Oreochromis_niloticus	CNR1	6	7	1
Oreochromis_niloticus	AKIRIN2	7	8	1
Oreochromis_niloticus	RARS2	8	9	1
Oreochromis_niloticus	SLC35A1	9	10	-1
Oreochromis_niloticus	LOC100692709	10	11	-1
Oreochromis_niloticus	LOC102081816	11	12	1
Scyliorhinus_canicula	SLC35A1	1	2	1
Scyliorhinus_canicula	RARS2	2	3	-1
Scyliorhinus_canicula	ORC3	3	4	1
Scyliorhinus_canicula	AKIRIN2	4	5	-1
Scyliorhinus_canicula	LOC119967921	5	6	1
Scyliorhinus_canicula	CNR1	6	7	-1
Scyliorhinus_canicula	RNGTT	7	8	-1
Scyliorhinus_canicula	LOC119967175	8	9	-1
Scyliorhinus_canicula	PNRC1	9	10	1
Scyliorhinus_canicula	LOC119967178	10	11	1
Scyliorhinus_canicula	LOC119967180	11	12	-1
Petromyzon_marinus	LOC116953416	1	2	-1
Petromyzon_marinus	LOC116953419	2	3	-1
Petromyzon_marinus	CEP162	3	4	1
Petromyzon_marinus	FBXL22	4	5	-1
Petromyzon_marinus	RNGTT	5	6	1
Petromyzon_marinus	CNR1	6	7	1
Petromyzon_marinus	AKIRIN2	7	8	1
Petromyzon_marinus	ORC3	8	9	-1
Petromyzon_marinus	RARS2	9	10	1
Petromyzon_marinus	SLC35A1	10	11	-1
Petromyzon_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?
在R中创建Sankey或Alluvial图,并在”next_node”和”next_x”值为”NA”时停止流动。

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()

在R中创建Sankey或Alluvial图,并在”next_node”和”next_x”值为”NA”时停止流动。

在R中创建Sankey或Alluvial图,并在”next_node”和”next_x”值为”NA”时停止流动。

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]])) %&gt;%
  filter(to != &quot;NA NA&quot;) %&gt;%
  as_tbl_graph() %&gt;%
  mutate(Species = str_replace(str_remove(name, &quot; .*&quot;), &quot;_&quot;, &quot;\n&quot;),
         Gene    = str_remove(name, &quot;.* &quot;),
         ypos    = as.numeric(factor(Gene)),
         xpos     = as.numeric(factor(Species, unique(Species)))) %&gt;%
  ggraph(layout = &quot;manual&quot;, 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 = &quot;none&quot;) +
  scale_edge_color_viridis(guide = &quot;none&quot;) +
  theme_void()

在R中创建Sankey或Alluvial图,并在”next_node”和”next_x”值为”NA”时停止流动。

You could even just do it as a dot-and-line plot:

library(tidyverse)

levs &lt;- names(sort(table(c(data$node, data$next_node))))

data %&gt;%
  mutate(x = gsub(&quot;_&quot;, &quot;\n&quot;, x), next_x = gsub(&quot;_&quot;, &quot;\n&quot;, next_x)) %&gt;%
  mutate(node = factor(node, levs), 
         next_node = factor(next_node, levs)) %&gt;%
  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 = &quot;none&quot;) +
  scale_y_discrete(limits = levs) +
  theme_minimal()

在R中创建Sankey或Alluvial图,并在”next_node”和”next_x”值为”NA”时停止流动。

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  • 本文由 发表于 2023年8月4日 01:30:28
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