Extract methylation information from dataframe for visualisation
Source:R/visualise_methylation.R
extract_methylation_from_dataframe.RdThis function takes a dataframe that contains methylation information in the form of
locations (indices along the read signifying bases at which modification probability
was assessed) and probabilities (the probability of modification at each assessed
location, as an integer from 0 to 255).
Each observation/row in the dataframe represents one sequence (e.g. a Nanopore read).
In the locations and probabilities column, each sequence (row) has many numbers associated.
These are stored as one string per observation e.g. "3,6,9,12", with the column representing
a character vector of such strings (e.g. c("3,6,9,12", "1,2,3,4")).
This function calls extract_and_sort_sequences() on each of these three columns and returns
a list of vectors stored in $locations, $probabilities, and $lengths.
These can then be used as input for visualise_methylation().
Default arguments are set up to work with the included example_many_sequences data.
Usage
extract_methylation_from_dataframe(
modification_data,
locations_colname = "methylation_locations",
probabilities_colname = "methylation_probabilities",
lengths_colname = "sequence_length",
grouping_levels = c(family = 8, individual = 2),
sort_by = "sequence_length",
desc_sort = TRUE
)Arguments
- modification_data
dataframe. A dataframe that must contain columns for methylation locations, methylation probabilities, and sequence length for each read. The former two should be condensed strings as produced byvector_to_string()e.g."1,2,3,4". The latter should be integer.
Seeexample_many_sequencesfor an example of a compatible dataframe.- locations_colname
character. The name of the column within the input dataframe that contains methylation/modification location information. Defaults to"methylation_locations".
Values within this column must be a comma-separated string representing a condensed numerical vector (e.g."3,6,9,12", produced viavector_to_string()) of the indices along the read at which modification was assessed. Indexing starts at 1.- probabilities_colname
character. The name of the column within the input dataframe that contains methylation/modification probability information. Defaults to"methylation_probabilities".
Values within this column must be a comma-separated string representing a condensed numerical vector (e.g."2,212,128,64", produced viavector_to_string()) of the probability of modification as an 8-bit (0-255) integer for each base where modification was assessed.- lengths_colname
character. The name of the column within the input dataframe that contains the length of each sequence. Defaults to"sequence_length".
Values within this column must be non-negative integers.- grouping_levels
named character vector. What variables should be used to define the groups/chunks, and how large a gap should be left between groups at that level. Set toNAto turn off grouping.
Defaults toc("family" = 8, "individual" = 2), meaning the highest-level groups are defined by thefamilycolumn, and there is a gap of 8 between each family. Likewise the second-level groups (within each family) are defined by theindividualcolumn, and there is a gap of 2 between each individual.
Any number of grouping variables and gaps can be given, as long as each grouping variable is a column within the dataframe. It is recommended that lower-level groups are more granular and subdivide higher-level groups (e.g. first divide into families, then into individuals within families).
To change the order of groups within a level, make that column a factor with the order specified e.g.example_many_sequences$family <- factor(example_many_sequences$family, levels = c("Family 2", "Family 3", "Family 1"))to change the order to Family 2, Family 3, Family 1.- sort_by
character. The name of the column within the dataframe that should be used to sort/order the rows within each lowest-level group. Set toNAto turn off sorting within groups.
Recommended to be the length of the sequence information, as is the case for the default"sequence_length"which was generated viaexample_many_sequences$sequence_legnth <- nchar(example_many_sequences$sequence).- desc_sort
logical. Boolean specifying whether rows within groups should be sorted by thesort_byvariable descending (TRUE, default) or ascending (FALSE).
Value
list, containing $locations (character vector), $probabilities (character vector), and $lengths (numeric vector).
Examples
## See documentation for extract_and_sort_sequences()
## for more examples of changing sorting/grouping
extract_methylation_from_dataframe(
example_many_sequences,
locations_colname = "methylation_locations",
probabilities_colname = "methylation_probabilities",
lengths_colname = "sequence_length",
grouping_levels = c("family" = 8, "individual" = 2),
sort_by = "sequence_length",
desc_sort = TRUE
)
#> $locations
#> [1] "3,6,9,12,15,18,21,24,27,36,39,42,51,54,57,66,69,72,81,84,87,96,99"
#> [2] "3,6,9,12,15,18,27,30,33,42,45,48,57,60,63,72,75,78,87,90"
#> [3] "3,6,9,12,15,18,21,24,27,36,39,42,51,54,57,66,69,72,81,84"
#> [4] "3,6,9,12,15,18,21,24,27,30,33,36,45,48,51,60,63,66,75,78"
#> [5] "3,6,9,12,15,18,21,24,27,30,33,42,45,48,57,60"
#> [6] ""
#> [7] ""
#> [8] "3,6,9,12,15,18,21,24,27,30,33,36,48,51,63,66"
#> [9] "3,6,9,12,15,18,21,24,27,30,42,45,57,60"
#> [10] ""
#> [11] ""
#> [12] "3,6,9,12,15,18,21,24,27,36,39,42,51,54,57,66,69,72,81,84"
#> [13] "3,6,9,12,15,18,21,24,27,36,39,42,51,54,57,66,69,78,81"
#> [14] "3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,54,57,60,69,72,75,78"
#> [15] ""
#> [16] ""
#> [17] ""
#> [18] ""
#> [19] ""
#> [20] ""
#> [21] ""
#> [22] ""
#> [23] "3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,75,78,87,90"
#> [24] ""
#> [25] ""
#> [26] "3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,75,84,87"
#> [27] "3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,81,84"
#> [28] "3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,78,81"
#> [29] ""
#> [30] ""
#> [31] ""
#> [32] ""
#> [33] ""
#> [34] ""
#> [35] ""
#> [36] ""
#> [37] "3,6,9,18,21,30,33,42,45,54,57,66,69,78,81,90,93"
#> [38] "3,6,9,12,15,18,21,30,33,42,45,54,57,66,69,78,81,90,93"
#> [39] ""
#> [40] ""
#> [41] "3,6,9,12,15,18,27,30,39,42,51,54,63,66,75,78,87,90"
#> [42] "3,6,9,12,15,18,27,30,39,42,51,54,63,66,75,78,87"
#> [43] "3,6,9,12,15,18,21,24,27,30,39,42,51,54,63,66,75,78,81,84"
#> [44] ""
#> [45] ""
#> [46] "3,6,9,12,15,18,21,30,33,42,45,54,57,66,69,78,81,90,93"
#> [47] ""
#> [48] ""
#> [49] "3,6,9,12,15,18,21,24,27,30,33,42,45,54,57,66,69,78,81,90,93"
#> [50] "3,6,9,12,15,18,21,24,33,36,45,48,57,60,69,72,81,84,87"
#> [51] "3,6,9,12,15,18,21,24,27,30,33,36,45,48,57,60,69,72,75,78"
#>
#> $probabilities
#> [1] "29,159,155,159,220,163,2,59,170,131,177,139,72,235,75,214,73,68,48,59,81,77,41"
#> [2] "170,236,120,36,139,50,229,99,79,41,229,42,230,34,34,27,130,77,7,79"
#> [3] "206,141,165,80,159,84,128,173,124,62,195,19,79,183,129,39,129,126,192,45"
#> [4] "216,221,11,81,4,61,180,79,130,13,144,31,228,4,200,23,132,98,18,82"
#> [5] "10,56,207,134,233,212,12,116,68,78,129,46,194,51,66,253"
#> [6] ""
#> [7] ""
#> [8] "31,56,233,241,71,31,203,190,234,254,240,124,72,64,128,127"
#> [9] "189,9,144,71,52,34,83,40,33,111,10,182,26,242"
#> [10] ""
#> [11] ""
#> [12] "81,245,162,32,108,233,119,232,152,161,222,128,251,83,123,91,160,189,144,250"
#> [13] "149,181,109,88,194,108,143,30,77,122,88,153,19,244,6,215,161,79,189"
#> [14] "147,112,58,21,217,60,252,153,255,96,142,110,147,110,57,22,163,110,19,205,83,193"
#> [15] ""
#> [16] ""
#> [17] ""
#> [18] ""
#> [19] ""
#> [20] ""
#> [21] ""
#> [22] ""
#> [23] "163,253,33,225,207,210,213,187,251,163,168,135,81,196,134,187,78,103,52,251,144,71,47,193,145,238,163,179"
#> [24] ""
#> [25] ""
#> [26] "191,91,194,96,204,7,129,209,139,68,88,94,109,234,200,188,72,116,73,178,209,167,105,243,62,155,193"
#> [27] "176,250,122,197,146,246,203,136,152,67,71,17,144,67,1,150,133,215,8,153,68,31,26,191,4,13"
#> [28] "122,217,108,8,66,85,34,127,205,86,130,126,203,145,27,206,145,54,191,78,125,252,108,62,55"
#> [29] ""
#> [30] ""
#> [31] ""
#> [32] ""
#> [33] ""
#> [34] ""
#> [35] ""
#> [36] ""
#> [37] "177,29,162,79,90,250,137,113,242,115,49,253,140,196,233,174,104"
#> [38] "104,37,50,49,104,89,213,51,220,101,39,87,94,109,48,168,235,187,225"
#> [39] ""
#> [40] ""
#> [41] "243,50,121,98,95,7,237,105,244,69,132,249,94,79,9,170,235,11"
#> [42] "51,190,33,181,255,241,151,186,124,196,1,142,117,84,213,249,168"
#> [43] "60,209,185,249,68,224,124,78,101,194,26,107,168,75,53,1,27,55,29,175"
#> [44] ""
#> [45] ""
#> [46] "49,251,241,176,189,187,166,43,235,144,137,5,93,175,106,193,198,146,48"
#> [47] ""
#> [48] ""
#> [49] "193,24,159,106,198,206,247,55,221,106,131,198,34,105,169,231,88,27,238,51,14"
#> [50] "161,156,9,65,198,255,245,191,174,63,155,146,13,95,228,100,132,45,49"
#> [51] "109,86,70,169,200,112,237,69,168,97,239,188,150,208,225,190,128,252,142,224"
#>
#> $lengths
#> [1] 102 93 87 81 63 0 0 69 63 0 0 87 84 81 0 0 0 0 0
#> [20] 0 0 0 93 0 0 90 87 84 0 0 0 0 0 0 0 0 96 96
#> [39] 0 0 93 90 87 0 0 96 0 0 96 90 81
#>
extract_methylation_from_dataframe(
example_many_sequences,
locations_colname = "hydroxymethylation_locations",
probabilities_colname = "hydroxymethylation_probabilities",
lengths_colname = "sequence_length",
grouping_levels = c("family" = 8, "individual" = 2),
sort_by = "sequence_length",
desc_sort = TRUE
)
#> $locations
#> [1] "3,6,9,12,15,18,21,24,27,36,39,42,51,54,57,66,69,72,81,84,87,96,99"
#> [2] "3,6,9,12,15,18,27,30,33,42,45,48,57,60,63,72,75,78,87,90"
#> [3] "3,6,9,12,15,18,21,24,27,36,39,42,51,54,57,66,69,72,81,84"
#> [4] "3,6,9,12,15,18,21,24,27,30,33,36,45,48,51,60,63,66,75,78"
#> [5] "3,6,9,12,15,18,21,24,27,30,33,42,45,48,57,60"
#> [6] ""
#> [7] ""
#> [8] "3,6,9,12,15,18,21,24,27,30,33,36,48,51,63,66"
#> [9] "3,6,9,12,15,18,21,24,27,30,42,45,57,60"
#> [10] ""
#> [11] ""
#> [12] "3,6,9,12,15,18,21,24,27,36,39,42,51,54,57,66,69,72,81,84"
#> [13] "3,6,9,12,15,18,21,24,27,36,39,42,51,54,57,66,69,78,81"
#> [14] "3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,54,57,60,69,72,75,78"
#> [15] ""
#> [16] ""
#> [17] ""
#> [18] ""
#> [19] ""
#> [20] ""
#> [21] ""
#> [22] ""
#> [23] "3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,75,78,87,90"
#> [24] ""
#> [25] ""
#> [26] "3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,75,84,87"
#> [27] "3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,81,84"
#> [28] "3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,78,81"
#> [29] ""
#> [30] ""
#> [31] ""
#> [32] ""
#> [33] ""
#> [34] ""
#> [35] ""
#> [36] ""
#> [37] "3,6,9,18,21,30,33,42,45,54,57,66,69,78,81,90,93"
#> [38] "3,6,9,12,15,18,21,30,33,42,45,54,57,66,69,78,81,90,93"
#> [39] ""
#> [40] ""
#> [41] "3,6,9,12,15,18,27,30,39,42,51,54,63,66,75,78,87,90"
#> [42] "3,6,9,12,15,18,27,30,39,42,51,54,63,66,75,78,87"
#> [43] "3,6,9,12,15,18,21,24,27,30,39,42,51,54,63,66,75,78,81,84"
#> [44] ""
#> [45] ""
#> [46] "3,6,9,12,15,18,21,30,33,42,45,54,57,66,69,78,81,90,93"
#> [47] ""
#> [48] ""
#> [49] "3,6,9,12,15,18,21,24,27,30,33,42,45,54,57,66,69,78,81,90,93"
#> [50] "3,6,9,12,15,18,21,24,33,36,45,48,57,60,69,72,81,84,87"
#> [51] "3,6,9,12,15,18,21,24,27,30,33,36,45,48,57,60,69,72,75,78"
#>
#> $probabilities
#> [1] "26,60,61,60,30,59,2,46,57,64,54,63,52,18,53,34,52,50,39,46,55,54,34"
#> [2] "57,18,64,31,63,40,23,61,55,34,23,35,23,30,29,24,64,53,7,54"
#> [3] "40,63,58,55,60,56,64,56,64,47,46,17,55,52,64,33,63,64,47,37"
#> [4] "33,29,10,55,3,46,53,54,64,12,63,27,24,4,43,21,64,60,17,55"
#> [5] "10,44,39,64,20,36,11,63,50,54,64,38,46,41,49,2"
#> [6] ""
#> [7] ""
#> [8] "27,44,20,13,51,28,41,48,19,1,14,64,52,48,64,64"
#> [9] "49,9,63,52,41,30,56,33,29,63,9,52,23,12"
#> [10] ""
#> [11] ""
#> [12] "55,10,59,28,62,20,64,21,62,59,29,64,4,56,64,59,60,49,63,5"
#> [13] "80,43,103,71,21,112,47,126,21,40,80,35,142,1,238,1,79,111,20"
#> [14] "62,63,45,19,32,46,3,61,0,159,42,80,46,84,86,52,8,92,102,4,138,20"
#> [15] ""
#> [16] ""
#> [17] ""
#> [18] ""
#> [19] ""
#> [20] ""
#> [21] ""
#> [22] ""
#> [23] "68,1,220,4,42,36,35,57,3,90,56,79,92,19,93,36,130,47,82,1,109,104,58,11,83,10,86,49"
#> [24] ""
#> [25] ""
#> [26] "3,123,22,121,19,198,3,23,95,102,45,55,54,9,51,53,135,39,83,22,32,72,98,5,184,24,38"
#> [27] "17,3,130,28,84,5,50,95,55,112,49,67,7,106,67,0,72,21,209,3,112,60,28,6,188,4"
#> [28] "93,18,125,104,6,44,74,17,25,136,42,66,26,88,129,5,89,114,14,133,40,1,145,82,49"
#> [29] ""
#> [30] ""
#> [31] ""
#> [32] ""
#> [33] ""
#> [34] ""
#> [35] ""
#> [36] ""
#> [37] "59,157,11,112,51,2,116,77,6,133,93,0,114,32,17,74,103"
#> [38] "61,89,30,41,29,68,15,170,7,133,86,26,55,54,88,16,13,63,22"
#> [39] ""
#> [40] ""
#> [41] "11,195,26,74,62,93,1,139,5,178,33,3,158,65,76,3,13,225"
#> [42] "9,13,165,10,0,10,104,65,78,43,124,87,0,95,19,2,73"
#> [43] "191,30,16,5,136,30,35,156,75,19,90,112,9,76,133,75,47,0,24,17"
#> [44] ""
#> [45] ""
#> [46] "24,3,3,78,63,47,66,155,13,19,109,141,87,2,55,43,24,83,161"
#> [47] ""
#> [48] ""
#> [49] "36,44,73,14,35,20,6,162,33,32,108,24,113,116,11,10,111,207,6,21,225"
#> [50] "52,87,155,117,2,0,3,50,81,184,75,74,60,97,15,8,46,188,81"
#> [51] "29,9,79,29,15,95,14,82,81,43,11,25,98,35,18,53,112,2,57,31"
#>
#> $lengths
#> [1] 102 93 87 81 63 0 0 69 63 0 0 87 84 81 0 0 0 0 0
#> [20] 0 0 0 93 0 0 90 87 84 0 0 0 0 0 0 0 0 96 96
#> [39] 0 0 93 90 87 0 0 96 0 0 96 90 81
#>