pathview - multiple states
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0
Entering edit mode
Philippine • 0
@e28160be
Last seen 10 hours ago
Canada

Hi folks,

I am trying to do a KEGG pathways using pathview in R.

Example of data

        data<- data.frame( 
EntrezID = c(107965807, 406114, 410747, 409341, 727522, 113218875, 410228, 113219265, 100576126, 102656882),
d3 = c(-1.8505053, -1.6865244, -1.5905482, -1.5222310, -1.4876187, -1.4257670, -1.3510711, -1.3431686, -1.3236289, -1.3113374),
d1 = c(NA, -1.0918122, -1.1389847, -0.9339650, NA, -1.1790280, -1.1046071, -1.2304113, NA, -0.9977286)
    )

Example with one state (using gene list)

d3 - extracting logFC and names for d3

geneList1=data$d3 # logFC (negative and positive)
names(geneList1)=data$EntrezID # entrezid for each gene

Run Pathview

pathview(gene.data  = geneList1,
         pathway.id = "ame04145",
         species    = "ame",
         na.col = "transparent",
         low = list(gene = "blue", cpd = "blue"), 
         mid =list(gene = "pink", cpd = "pink"), 
         high = list(gene = "red", cpd ="red"),
         limit = list(gene = 3), 
         bins = list(gene = 10), 
         both.dirs = list(gene = T),
         out.suffix="_d1"
         )

Very nice plot with gene modulated colored as asked

Comparing two states (d1 and d3)

rownames(data)=data$EntrezID 
pathview(gene.data = data[,2:3], 
                           limit = list(gene = 3), 
                           bins = list(gene = 10), 
                           both.dirs = list(gene = T),
                           pathway.id = "ame04145",
                           species = "ame", 
                           keys.align = "y", 
                           kegg.native = T, 
                           match.data = T,
                            same.layer = T,
                           multi.state = T, out.suffix="mixed")

Output

Warning: None of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong.
Warning: No annotation package for the species ame, gene symbols not mapped!
Info: Working in directory /Users/camilledeboissel/Library/CloudStorage/OneDrive-Personal/Post-doc/Amro-Zayed_BeeCSI/Phiphi_analysis/All_samples_analysis
Info: Writing image file ame04145.mixed.png
Warning message:
In colnames(plot.data)[c(1, 3, 9:ncs)] <- c("kegg.names", "all.mapped",  :
  number of items to replace is not a multiple of replacement length

What am I doing wrong here? Why is it working with a geneList input and not as multistate ?

Thank you for your help
pathview Pathways KEGG • 220 views
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A quick comment after I copied/pasted your code: when using geneList1 in the 3rd code chunk I do not get a nice plot... I rather got the same error that none of the ids mapped to the pathway! Yet, it does work when mapping to pathway.id = "ame00500"! Note that in your code chunk you used as input geneList (thus without the suffix 1!)

Thus: your example input can indeed not be mapped on pathway ame04145.

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Entering edit mode

Thank you! Here a subset of genes that really works with "ame04145".

data <- data.frame(
  EntrezID = c(100577548, 100577764, 406097, 408388, 408782, 409055, 409074, 409165, 409946, 410510,
               410614, 410994, 410996, 411295, 411519, 411816, 411892, 412810, 412886, 413394, 413409,
               550827, 551093, 551176, 551369, 551467, 551721, 551961, 552410, 552419, 552476, 552720,
               552756, 724873, 725404, 725770, 727630),
  d3 = c(-0.3160703, 0.1744582, 0.2486408, 0.3705891, 0.4113416, -0.138168, -0.1286653, 0.2179565, -0.25528,
         0.1109674, -0.447057, -0.2836039, -0.4338239, -0.1359435, 0.4601004, 0.1777216, -0.1788376, -0.3106547,
         0.3039518, 0.121097, 0.1156489, 0.2935189, -0.1476104, -0.3896508, -0.4518688, -0.1381761, -0.1364185,
         -0.2484124, -0.1674127, 0.1881968, -0.1057918, -0.2627917, -0.2030586, 0.100829, -0.2246011, 0.1204396,
         -0.2196931),
  d1 = c(NA, 0.1612697, NA, NA, 0.2773722, -0.1260812, -0.1465551, NA, -0.2141968, NA, NA, NA, NA, -0.1331895,
         NA, NA, NA, -0.3220328, NA, NA, 0.1060707, NA, -0.1569927, -0.3378576, -0.3689568, NA, NA, NA, -0.1658039,
         0.1535351, NA, -0.2494884, -0.1717161, NA, NA, 0.1328381, -0.1424635)
)

I run

geneList=data$d1
names(geneList)=data$EntrezID
pathview(gene.data  = geneList,
         pathway.id = "ame04145",
         species    = "ame",
         na.col = "transparent",
         low = list(gene = "blue", cpd = "blue"), 
         mid =list(gene = "pink", cpd = "pink"), 
         high = list(gene = "red", cpd ="red"),
         limit = list(gene = 3), 
         bins = list(gene = 10), 
         both.dirs = list(gene = T),
         out.suffix="_d1"
         )

Info: Downloading xml files for ame04145, 1/1 pathways..
Info: Downloading png files for ame04145, 1/1 pathways..
Warning: No annotation package for the species ame, gene symbols not mapped!

And this i my actual output enter image description here

When I run

rownames(data)=data$EntrezID
pathview(gene.data  = data[,2:3],
         pathway.id = "ame04145",
         species    = "ame",
         na.col = "transparent",
         low = list(gene = "blue", cpd = "blue"), 
         mid =list(gene = "pink", cpd = "pink"), 
         high = list(gene = "red", cpd ="red"),
         limit = list(gene = 3), 
         bins = list(gene = 10), 
         both.dirs = list(gene = T),
         out.suffix="_d1"
         )

Warning: None of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong.
Warning: No annotation package for the species ame, gene symbols not mapped!

And I got this pawthay... enter image description here

So i am not sure what I am missing here. Thanks for your feedback

ADD REPLY •
1
Entering edit mode

According to the the help page of pathview (type ?pathview) the input should be either vector (single sample) or a matrix-like data (multiple sample). Note that your input is a data.frame. Converting this to a matrix makes your code work, taking into account the NA.

> library(pathview)
> 
> data <- data.frame(
+   EntrezID = c(100577548, 100577764, 406097, 408388, 408782, 409055, 409074, 409165, 409946, 410510,
+                410614, 410994, 410996, 411295, 411519, 411816, 411892, 412810, 412886, 413394, 413409,
+                550827, 551093, 551176, 551369, 551467, 551721, 551961, 552410, 552419, 552476, 552720,
+                552756, 724873, 725404, 725770, 727630),
+   d3 = c(-0.3160703, 0.1744582, 0.2486408, 0.3705891, 0.4113416, -0.138168, -0.1286653, 0.2179565, -0.25528,
+          0.1109674, -0.447057, -0.2836039, -0.4338239, -0.1359435, 0.4601004, 0.1777216, -0.1788376, -0.3106547,
+          0.3039518, 0.121097, 0.1156489, 0.2935189, -0.1476104, -0.3896508, -0.4518688, -0.1381761, -0.1364185,
+          -0.2484124, -0.1674127, 0.1881968, -0.1057918, -0.2627917, -0.2030586, 0.100829, -0.2246011, 0.1204396,
+          -0.2196931),
+   d1 = c(NA, 0.1612697, NA, NA, 0.2773722, -0.1260812, -0.1465551, NA, -0.2141968, NA, NA, NA, NA, -0.1331895,
+          NA, NA, NA, -0.3220328, NA, NA, 0.1060707, NA, -0.1569927, -0.3378576, -0.3689568, NA, NA, NA, -0.1658039,
+          0.1535351, NA, -0.2494884, -0.1717161, NA, NA, 0.1328381, -0.1424635)
+ )
> 
> class(data)
[1] "data.frame"
> head(data)
   EntrezID         d3         d1
1 100577548 -0.3160703         NA
2 100577764  0.1744582  0.1612697
3    406097  0.2486408         NA
4    408388  0.3705891         NA
5    408782  0.4113416  0.2773722
6    409055 -0.1381680 -0.1260812
> 
> ## convert to matrix, but do not include 1st column
> matrix.data <- as.matrix(data[,-1])
> 
> ## use 1st column as rownames for matrix
> rownames(matrix.data) <- data[,1]
> 
> class(matrix.data)
[1] "matrix" "array" 
> head(matrix.data)
                  d3         d1
100577548 -0.3160703         NA
100577764  0.1744582  0.1612697
406097     0.2486408         NA
408388     0.3705891         NA
408782     0.4113416  0.2773722
409055    -0.1381680 -0.1260812
> 
> ## run pathview
> ## note that the 2 columns are explicitly defined, but since the
> ## data sets consists only of 2 samples this would not be needed now.
> pathview(gene.data  = matrix.data[,1:2],
+          pathway.id = "ame04145",
+          species    = "ame",
+          na.col = "transparent",
+          low = list(gene = "blue", cpd = "blue"), 
+          mid =list(gene = "pink", cpd = "pink"), 
+          high = list(gene = "red", cpd ="red"),
+          limit = list(gene = 3), 
+          bins = list(gene = 10), 
+          both.dirs = list(gene = T),
+          out.suffix="_d1"
+          )
Warning: No annotation package for the species ame, gene symbols not mapped!
Info: Working in directory xx:/yy
Info: Writing image file ame04145._d1.multi.png
> 
>

enter image description here

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0
Entering edit mode

:D Thank you!!! It works perfectly.

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