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mayoverse / kinship2

Pedigree creation, plotting, and analytics
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Plotting problem in 1.9.1. #11

Closed magnusdv closed 1 year ago

magnusdv commented 1 year ago

The following pedigrees plot nicely with the CRAN version (1.8.5) but not with the current dev version (1.9.1):

Version 1.8.5 (good)

library(kinship2, quietly = T)
packageVersion("kinship2")
#> [1] '1.8.5'

x1 = pedigree(id = 1:4, dad = c(0,0,1,3), mom = c(0,0,2,2), sex = c(1,2,1,1))
x2 = pedigree(id = 1:7, dad = c(0,0,1,1,1,1,3), mom = c(0,0,2,2,2,2,2), 
              sex = c(1,2,1,1,1,1,1))

par(mfrow = c(1,2))
plot(x1, mar = c(1,2,1,2))
plot(x2, mar = c(1,2,1,2))

Created on 2022-09-21 with reprex v2.0.2

Version 1.9.1 (bad)

library(kinship2, quietly = T)
packageVersion("kinship2")
#> [1] '1.9.1'

The first plots badly:

plot(x1)

The second does not plot at all:

plot(x2)
#> Error in myid[i, rval$nid[i, ] > 0] <- cumsum(c(0, rval$n))[i] + 1:rval$n[i]: number of items to replace is not a multiple of replacement length

Created on 2022-09-21 with reprex v2.0.2

I'm pretty sure the error lies in kindepth(..., align = TRUE) which gives different outputs in the two versions.

sinnweja commented 1 year ago

Thanks, I'm making updates to the github version and preparing for an update to CRAN soon. I'll check this one before I upload, and make sure I did not break anything in 1.9.1.

From: Magnus Dehli Vigeland @.> Sent: Wednesday, September 21, 2022 6:55 AM To: mayoverse/kinship2 @.> Cc: Subscribed @.***> Subject: [EXTERNAL] [mayoverse/kinship2] Plotting problem in 1.9.1. (Issue #11)

The following pedigrees plot nicely with the CRAN version (1.8.5) but not with the current dev version (1.9.1):

Version 1.8.5 (good)

library(kinship2, quietly = T)

packageVersion("kinship2")

> [1] '1.8.5'

x1 = pedigree(id = 1:4, dad = c(0,0,1,3), mom = c(0,0,2,2), sex = c(1,2,1,1))

x2 = pedigree(id = 1:7, dad = c(0,0,1,1,1,1,3), mom = c(0,0,2,2,2,2,2),

          sex = c(1,2,1,1,1,1,1))

par(mfrow = c(1,2))

plot(x1, mar = c(1,2,1,2))

plot(x2, mar = c(1,2,1,2))

[https://camo.githubusercontent.com/499cce94fd859e7414c9b493c3a3a3b039424320544d2cb2c6b43a516137f002/68747470733a2f2f692e696d6775722e636f6d2f356639557747612e706e67]https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcamo.githubusercontent.com%2F499cce94fd859e7414c9b493c3a3a3b039424320544d2cb2c6b43a516137f002%2F68747470733a2f2f692e696d6775722e636f6d2f356639557747612e706e67&data=05%7C01%7CSinnwell.Jason%40mayo.edu%7Cd79d03483e464646ad1008da9bc820a1%7Ca25fff9c3f634fb29a8ad9bdd0321f9a%7C0%7C0%7C637993581087316792%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=YVNe7ymzj0QKc5D08VRdUV5cADkAbQ%2BGpRbpiUGdQC8%3D&reserved=0

Created on 2022-09-21 with reprex v2.0.2https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Freprex.tidyverse.org%2F&data=05%7C01%7CSinnwell.Jason%40mayo.edu%7Cd79d03483e464646ad1008da9bc820a1%7Ca25fff9c3f634fb29a8ad9bdd0321f9a%7C0%7C0%7C637993581087316792%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8VDREe9AB8X%2FB7NehKZJWe6aQ3MlMA2X6sTNTGhO1ho%3D&reserved=0

Version 1.9.1 (bad)

library(kinship2, quietly = T)

packageVersion("kinship2")

> [1] '1.9.1'

The first plots badly:

plot(x1)

[https://camo.githubusercontent.com/27225e3b77f62da540ed292c0a7ae4bd20bf3b3afe7e05aec980c17ea5874ab5/68747470733a2f2f692e696d6775722e636f6d2f445a6c476e66472e706e67]https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcamo.githubusercontent.com%2F27225e3b77f62da540ed292c0a7ae4bd20bf3b3afe7e05aec980c17ea5874ab5%2F68747470733a2f2f692e696d6775722e636f6d2f445a6c476e66472e706e67&data=05%7C01%7CSinnwell.Jason%40mayo.edu%7Cd79d03483e464646ad1008da9bc820a1%7Ca25fff9c3f634fb29a8ad9bdd0321f9a%7C0%7C0%7C637993581087316792%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=T4DsfoTL%2BVhWFFOm0dYlWuydiCwKR30XbPp2ccUT1GA%3D&reserved=0

The second does not plot at all:

plot(x2)

> Error in myid[i, rval$nid[i, ] > 0] <- cumsum(c(0, rval$n))[i] + 1:rval$n[i]: number of items to replace is not a multiple of replacement length

Created on 2022-09-21 with reprex v2.0.2https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Freprex.tidyverse.org%2F&data=05%7C01%7CSinnwell.Jason%40mayo.edu%7Cd79d03483e464646ad1008da9bc820a1%7Ca25fff9c3f634fb29a8ad9bdd0321f9a%7C0%7C0%7C637993581087316792%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8VDREe9AB8X%2FB7NehKZJWe6aQ3MlMA2X6sTNTGhO1ho%3D&reserved=0

I'm pretty sure the error lies in kindepth(..., align = TRUE) which gives different outputs in the two versions.

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