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library(MiscMetabar)
#> Warning: replacing previous import 'S4Arrays::makeNindexFromArrayViewport' by
#> 'DelayedArray::makeNindexFromArrayViewport' when loading 'SummarizedExperiment'
data(data_fungi)
summary_plot_pq(data_fungi)

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sam_tab <- tibble::as_tibble(unclass(data_fungi@sam_data))
summarytools::dfSummary(sam_tab)
#> Warning: no DISPLAY variable so Tk is not available
#> Warning in png(png_loc <- tempfile(fileext = ".png"), width = 150 *
#> graph.magnif, : unable to open connection to X11 display ''

#> Warning in png(png_loc <- tempfile(fileext = ".png"), width = 150 *
#> graph.magnif, : unable to open connection to X11 display ''

#> Warning in png(png_loc <- tempfile(fileext = ".png"), width = 150 *
#> graph.magnif, : unable to open connection to X11 display ''
#> Warning in png(png_loc <- tempfile(fileext = ".png"), width = 150 *
#> graph.magnif, : unable to open connection to X11 display ''
#> Warning in png(png_loc <- tempfile(fileext = ".png"), width = 150 *
#> graph.magnif, : unable to open connection to X11 display ''

#> Warning in png(png_loc <- tempfile(fileext = ".png"), width = 150 *
#> graph.magnif, : unable to open connection to X11 display ''

#> Warning in png(png_loc <- tempfile(fileext = ".png"), width = 150 *
#> graph.magnif, : unable to open connection to X11 display ''
#> Data Frame Summary  
#> sam_tab  
#> Dimensions: 185 x 7  
#> Duplicates: 0  
#> 
#> --------------------------------------------------------------------------------------------------------------------
#> No   Variable       Stats / Values                  Freqs (% of Valid)    Graph                 Valid      Missing  
#> ---- -------------- ------------------------------- --------------------- --------------------- ---------- ---------
#> 1    X              1. A10-005-B_S188_MERGED.fas      1 ( 0.5%)                                 185        0        
#>      [character]    2. A10-005-H_S189_MERGED.fas      1 ( 0.5%)                                 (100.0%)   (0.0%)   
#>                     3. A10-005-M_S190_MERGED.fas      1 ( 0.5%)                                                     
#>                     4. A12-007_S191_MERGED.fastq      1 ( 0.5%)                                                     
#>                     5. A12-007-B_S2_MERGED.fastq      1 ( 0.5%)                                                     
#>                     6. A15-004_S3_MERGED.fastq.g      1 ( 0.5%)                                                     
#>                     7. A8-005_S4_MERGED.fastq.gz      1 ( 0.5%)                                                     
#>                     8. A9-012_S5_MERGED.fastq.gz      1 ( 0.5%)                                                     
#>                     9. AB29-ABMX-H_S6_MERGED.fas      1 ( 0.5%)                                                     
#>                     10. AC27-013_S7_MERGED.fastq.     1 ( 0.5%)                                                     
#>                     [ 175 others ]                  175 (94.6%)           IIIIIIIIIIIIIIIIII                        
#> 
#> 2    Sample_names   1. A10-005-B_S188                 1 ( 0.5%)                                 185        0        
#>      [character]    2. A10-005-H_S189                 1 ( 0.5%)                                 (100.0%)   (0.0%)   
#>                     3. A10-005-M_S190                 1 ( 0.5%)                                                     
#>                     4. A12-007_S191                   1 ( 0.5%)                                                     
#>                     5. A12-007-B_S2                   1 ( 0.5%)                                                     
#>                     6. A15-004_S3                     1 ( 0.5%)                                                     
#>                     7. A8-005_S4                      1 ( 0.5%)                                                     
#>                     8. A9-012_S5                      1 ( 0.5%)                                                     
#>                     9. AB29-ABMX-H_S6                 1 ( 0.5%)                                                     
#>                     10. AC27-013_S7                   1 ( 0.5%)                                                     
#>                     [ 175 others ]                  175 (94.6%)           IIIIIIIIIIIIIIIIII                        
#> 
#> 3    Tree_name      1. AD30-abm-X                     4 ( 2.2%)                                 185        0        
#>      [character]    2. A10-005                        3 ( 1.6%)                                 (100.0%)   (0.0%)   
#>                     3. AD26-005                       3 ( 1.6%)                                                     
#>                     4. BB6-019                        3 ( 1.6%)                                                     
#>                     5. BE9-006                        3 ( 1.6%)                                                     
#>                     6. BG7-010                        3 ( 1.6%)                                                     
#>                     7. BL7-006                        3 ( 1.6%)                                                     
#>                     8. BP11-001                       3 ( 1.6%)                                                     
#>                     9. BQ4-018                        3 ( 1.6%)                                                     
#>                     10. BU11-002                      3 ( 1.6%)                                                     
#>                     [ 102 others ]                  154 (83.2%)           IIIIIIIIIIIIIIII                          
#> 
#> 4    Sample_id      Mean (sd) : 96.5 (55.7)         185 distinct values   : : : . :   : : : :   185        0        
#>      [integer]      min < med < max:                                      : : : : : : : : : :   (100.0%)   (0.0%)   
#>                     2 < 96 < 191                                          : : : : : : : : : :                       
#>                     IQR (CV) : 97 (0.6)                                   : : : : : : : : : :                       
#>                                                                           : : : : : : : : : :                       
#> 
#> 5    Height         1. High                         41 (31.3%)            IIIIII                131        54       
#>      [character]    2. Low                          45 (34.4%)            IIIIII                (70.8%)    (29.2%)  
#>                     3. Middle                       45 (34.4%)            IIIIII                                    
#> 
#> 6    Diameter       1. 30                            13 ( 7.2%)           I                     180        5        
#>      [character]    2. 25                             8 ( 4.4%)                                 (97.3%)    (2.7%)   
#>                     3. -                              6 ( 3.3%)                                                     
#>                     4. 34                             6 ( 3.3%)                                                     
#>                     5. 32                             5 ( 2.8%)                                                     
#>                     6. 40                             5 ( 2.8%)                                                     
#>                     7. 52                             5 ( 2.8%)                                                     
#>                     8. 21,5                           4 ( 2.2%)                                                     
#>                     9. 33,3                           4 ( 2.2%)                                                     
#>                     10. 33,5                          4 ( 2.2%)                                                     
#>                     [ 67 others ]                   120 (66.7%)           IIIIIIIIIIIII                             
#> 
#> 7    Time           Mean (sd) : 5.8 (5.9)           0 : 67 (41.4%)        IIIIIIII              162        23       
#>      [integer]      min < med < max:                5 : 38 (23.5%)        IIII                  (87.6%)    (12.4%)  
#>                     0 < 5 < 15                      10 : 21 (13.0%)       II                                        
#>                     IQR (CV) : 10 (1)               15 : 36 (22.2%)       IIII                                      
#> --------------------------------------------------------------------------------------------------------------------
datawizard::data_codebook(sam_tab)
#> sam_tab (185 rows and 7 variables, 7 shown)
#> 
#> ID | Name         | Type      |   Missings |                         Values |          N
#> ---+--------------+-----------+------------+--------------------------------+-----------
#> 1  | X            | character |   0 (0.0%) | A10-005-B_S188_MERGED.fastq.gz |  1 ( 0.5%)
#>    |              |           |            | A10-005-H_S189_MERGED.fastq.gz |  1 ( 0.5%)
#>    |              |           |            | A10-005-M_S190_MERGED.fastq.gz |  1 ( 0.5%)
#>    |              |           |            |   A12-007_S191_MERGED.fastq.gz |  1 ( 0.5%)
#>    |              |           |            |   A12-007-B_S2_MERGED.fastq.gz |  1 ( 0.5%)
#>    |              |           |            |     A15-004_S3_MERGED.fastq.gz |  1 ( 0.5%)
#>    |              |           |            |      A8-005_S4_MERGED.fastq.gz |  1 ( 0.5%)
#>    |              |           |            |      A9-012_S5_MERGED.fastq.gz |  1 ( 0.5%)
#>    |              |           |            | AB29-ABMX-H_S6_MERGED.fastq.gz |  1 ( 0.5%)
#>    |              |           |            |    AC27-013_S7_MERGED.fastq.gz |  1 ( 0.5%)
#>    |              |           |            |                          (...) |           
#> ---+--------------+-----------+------------+--------------------------------+-----------
#> 2  | Sample_names | character |   0 (0.0%) |                 A10-005-B_S188 |  1 ( 0.5%)
#>    |              |           |            |                 A10-005-H_S189 |  1 ( 0.5%)
#>    |              |           |            |                 A10-005-M_S190 |  1 ( 0.5%)
#>    |              |           |            |                   A12-007_S191 |  1 ( 0.5%)
#>    |              |           |            |                   A12-007-B_S2 |  1 ( 0.5%)
#>    |              |           |            |                     A15-004_S3 |  1 ( 0.5%)
#>    |              |           |            |                      A8-005_S4 |  1 ( 0.5%)
#>    |              |           |            |                      A9-012_S5 |  1 ( 0.5%)
#>    |              |           |            |                 AB29-ABMX-H_S6 |  1 ( 0.5%)
#>    |              |           |            |                    AC27-013_S7 |  1 ( 0.5%)
#>    |              |           |            |                          (...) |           
#> ---+--------------+-----------+------------+--------------------------------+-----------
#> 3  | Tree_name    | character |   0 (0.0%) |                        A10-005 |  3 ( 1.6%)
#>    |              |           |            |                        A12-007 |  2 ( 1.1%)
#>    |              |           |            |                        A15-004 |  1 ( 0.5%)
#>    |              |           |            |                         A8-005 |  1 ( 0.5%)
#>    |              |           |            |                         A9-012 |  1 ( 0.5%)
#>    |              |           |            |                     AB29-abm-X |  1 ( 0.5%)
#>    |              |           |            |                       AC27-013 |  1 ( 0.5%)
#>    |              |           |            |                       AC29-033 |  1 ( 0.5%)
#>    |              |           |            |                       AD26-005 |  3 ( 1.6%)
#>    |              |           |            |                     AD30-abm-X |  4 ( 2.2%)
#>    |              |           |            |                          (...) |           
#> ---+--------------+-----------+------------+--------------------------------+-----------
#> 4  | Sample_id    | integer   |   0 (0.0%) |                       [2, 191] |        185
#> ---+--------------+-----------+------------+--------------------------------+-----------
#> 5  | Height       | character | 54 (29.2%) |                           High | 41 (31.3%)
#>    |              |           |            |                            Low | 45 (34.4%)
#>    |              |           |            |                         Middle | 45 (34.4%)
#> ---+--------------+-----------+------------+--------------------------------+-----------
#> 6  | Diameter     | character |   5 (2.7%) |                              - |  6 ( 3.3%)
#>    |              |           |            |                             10 |  2 ( 1.1%)
#>    |              |           |            |                             11 |  2 ( 1.1%)
#>    |              |           |            |                          115,5 |  3 ( 1.7%)
#>    |              |           |            |                           18,3 |  1 ( 0.6%)
#>    |              |           |            |                           18,4 |  1 ( 0.6%)
#>    |              |           |            |                           18,9 |  3 ( 1.7%)
#>    |              |           |            |                             20 |  3 ( 1.7%)
#>    |              |           |            |                           21,5 |  4 ( 2.2%)
#>    |              |           |            |                             23 |  1 ( 0.6%)
#>    |              |           |            |                          (...) |           
#> ---+--------------+-----------+------------+--------------------------------+-----------
#> 7  | Time         | integer   | 23 (12.4%) |                              0 | 67 (41.4%)
#>    |              |           |            |                              5 | 38 (23.5%)
#>    |              |           |            |                             10 | 21 (13.0%)
#>    |              |           |            |                             15 | 36 (22.2%)
#> ----------------------------------------------------------------------------------------
pillar::glimpse(sam_tab)
#> Rows: 185
#> Warning in class(x) <- tibble_class: Setting class(x) to multiple strings
#> ("tbl_df", "tbl", ...); result will no longer be an S4 object
#> Columns: 7
#> $ X            <chr> "A10-005-B_S188_MERGED.fastq.gz", "A10-005-H_S189_MERGED.…
#> $ Sample_names <chr> "A10-005-B_S188", "A10-005-H_S189", "A10-005-M_S190", "A1…
#> $ Tree_name    <chr> "A10-005", "A10-005", "A10-005", "A12-007", "A12-007", "A…
#> $ Sample_id    <int> 188, 189, 190, 191, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 1…
#> $ Height       <chr> "Low", "High", "Middle", NA, "Low", NA, NA, NA, "High", N…
#> $ Diameter     <chr> "52", "52", "52", "28,4", "28,4", "30,7", "32,8", "33,3",…
#> $ Time         <int> 15, 15, 15, 0, 0, 0, 0, 0, 5, 15, 15, 15, 15, 15, 5, NA, …
pointblank::scan_data(sam_tab, sections = "OVSCMI")
#> Warning in class(x) <- tibble_class: Setting class(x) to multiple strings
#> ("tbl_df", "tbl", ...); result will no longer be an S4 object

Table Overview

Columns

7

Rows

185

NAs

82 (6.33%)

Duplicate Rows

0

Column Types

character 5
integer 2

Reproducibility Information

Scan Build Time

2024-02-13 13:06:30

pointblank Version

0.11.4

R Version

R version 4.3.2 (2023–10–31)
Eye Holes

Operating System

x86_64-pc-linux-gnu

Distinct

185

NAs

0

Inf/-Inf

0

Distinct

185

NAs

0

Inf/-Inf

0

Distinct

112

NAs

0

Inf/-Inf

0

Distinct

185

NAs

0

Inf/-Inf

0

Mean

96.5

Minimum

2

Maximum

191

Distinct

4

NAs

54

Inf/-Inf

0

Distinct

78

NAs

5

Inf/-Inf

0

Distinct

5

NAs

23

Inf/-Inf

0

Mean

5.8

Minimum

0

Maximum

15
X Sample_names Tree_name Sample_id Height Diameter Time
1 A10-005-B_S188_MERGED.fastq.gz A10-005-B_S188 A10-005 188 Low 52 15
2 A10-005-H_S189_MERGED.fastq.gz A10-005-H_S189 A10-005 189 High 52 15
3 A10-005-M_S190_MERGED.fastq.gz A10-005-M_S190 A10-005 190 Middle 52 15
4 A12-007_S191_MERGED.fastq.gz A12-007_S191 A12-007 191 NA 28,4 0
5 A12-007-B_S2_MERGED.fastq.gz A12-007-B_S2 A12-007 2 Low 28,4 0
6..180
181 Y29-007-M_S183_MERGED.fastq.gz Y29-007-M_S183 Y29-007 183 Middle 68,6 0
182 Y31-ABM484-B_S184_MERGED.fastq.gz Y31-ABM484-B_S184 Y31-abm484 184 Low 20 5
183 Z29-001-H_S185_MERGED.fastq.gz Z29-001-H_S185 Z29-001 185 High 35,2 5
184 Z30-002_S186_MERGED.fastq.gz Z30-002_S186 Z30-002 186 NA 43,4 15
185 Z30-ABM560-M_S187_MERGED.fastq.gz Z30-ABM560-M_S187 Z30-abm560 187 Middle 11 5