tests/testthat/_snaps/intermediate_qc_plots.md

In cancerit/RCRISPR: R Functions for CRISPR-Related Analyses

can plot common violin, all samples

Code
  p$data
Output
                         sgRNA gene         sample values
  1  A1BG_CACCTTCGAGCTGCTGCGCG A1BG        HELA_T0    478
  2  A1BG_AAGAGCGCCTCGGTCCCAGC A1BG        HELA_T0      0
  3  A1BG_TGGACTTCCAGCTACGGCGC A1BG        HELA_T0    274
  4  A1BG_CACCTTCGAGCTGCTGCGCG A1BG HELA_T15A_CTRL    519
  5  A1BG_AAGAGCGCCTCGGTCCCAGC A1BG HELA_T15A_CTRL      0
  6  A1BG_TGGACTTCCAGCTACGGCGC A1BG HELA_T15A_CTRL    193
  7  A1BG_CACCTTCGAGCTGCTGCGCG A1BG HELA_T15B_CTRL    439
  8  A1BG_AAGAGCGCCTCGGTCCCAGC A1BG HELA_T15B_CTRL      0
  9  A1BG_TGGACTTCCAGCTACGGCGC A1BG HELA_T15B_CTRL    163
  10 A1BG_CACCTTCGAGCTGCTGCGCG A1BG HELA_T15C_CTRL    587
  11 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG HELA_T15C_CTRL     52
  12 A1BG_TGGACTTCCAGCTACGGCGC A1BG HELA_T15C_CTRL    161
  13 A1BG_CACCTTCGAGCTGCTGCGCG A1BG  HELA_T15A_OLA    389
  14 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG  HELA_T15A_OLA      0
  15 A1BG_TGGACTTCCAGCTACGGCGC A1BG  HELA_T15A_OLA     80
  16 A1BG_CACCTTCGAGCTGCTGCGCG A1BG  HELA_T15B_OLA    591
  17 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG  HELA_T15B_OLA     16
  18 A1BG_TGGACTTCCAGCTACGGCGC A1BG  HELA_T15B_OLA    393
  19 A1BG_CACCTTCGAGCTGCTGCGCG A1BG  HELA_T15C_OLA    274
  20 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG  HELA_T15C_OLA      0
  21 A1BG_TGGACTTCCAGCTACGGCGC A1BG  HELA_T15C_OLA     45

Code
  p$layers
Output
  [[1]]
  geom_violin: draw_quantiles = NULL, na.rm = FALSE, orientation = NA
  stat_ydensity: trim = TRUE, scale = area, na.rm = FALSE, orientation = NA
  position_dodge

can plot common violin, with groups

Code
  p$data
Output
                         sgRNA gene         sample values          group
  1  A1BG_CACCTTCGAGCTGCTGCGCG A1BG        HELA_T0    478        HELA_T0
  2  A1BG_AAGAGCGCCTCGGTCCCAGC A1BG        HELA_T0      0        HELA_T0
  3  A1BG_TGGACTTCCAGCTACGGCGC A1BG        HELA_T0    274        HELA_T0
  4  A1BG_CACCTTCGAGCTGCTGCGCG A1BG HELA_T15A_CTRL    519 HELA_T15A_CTRL
  5  A1BG_AAGAGCGCCTCGGTCCCAGC A1BG HELA_T15A_CTRL      0 HELA_T15A_CTRL
  6  A1BG_TGGACTTCCAGCTACGGCGC A1BG HELA_T15A_CTRL    193 HELA_T15A_CTRL
  7  A1BG_CACCTTCGAGCTGCTGCGCG A1BG HELA_T15B_CTRL    439 HELA_T15B_CTRL
  8  A1BG_AAGAGCGCCTCGGTCCCAGC A1BG HELA_T15B_CTRL      0 HELA_T15B_CTRL
  9  A1BG_TGGACTTCCAGCTACGGCGC A1BG HELA_T15B_CTRL    163 HELA_T15B_CTRL
  10 A1BG_CACCTTCGAGCTGCTGCGCG A1BG HELA_T15C_CTRL    587 HELA_T15C_CTRL
  11 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG HELA_T15C_CTRL     52 HELA_T15C_CTRL
  12 A1BG_TGGACTTCCAGCTACGGCGC A1BG HELA_T15C_CTRL    161 HELA_T15C_CTRL
  13 A1BG_CACCTTCGAGCTGCTGCGCG A1BG  HELA_T15A_OLA    389  HELA_T15A_OLA
  14 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG  HELA_T15A_OLA      0  HELA_T15A_OLA
  15 A1BG_TGGACTTCCAGCTACGGCGC A1BG  HELA_T15A_OLA     80  HELA_T15A_OLA
  16 A1BG_CACCTTCGAGCTGCTGCGCG A1BG  HELA_T15B_OLA    591  HELA_T15B_OLA
  17 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG  HELA_T15B_OLA     16  HELA_T15B_OLA
  18 A1BG_TGGACTTCCAGCTACGGCGC A1BG  HELA_T15B_OLA    393  HELA_T15B_OLA
  19 A1BG_CACCTTCGAGCTGCTGCGCG A1BG  HELA_T15C_OLA    274  HELA_T15C_OLA
  20 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG  HELA_T15C_OLA      0  HELA_T15C_OLA
  21 A1BG_TGGACTTCCAGCTACGGCGC A1BG  HELA_T15C_OLA     45  HELA_T15C_OLA

Code
  p$layers
Output
  [[1]]
  geom_violin: draw_quantiles = NULL, na.rm = FALSE, orientation = NA
  stat_ydensity: trim = TRUE, scale = area, na.rm = FALSE, orientation = NA
  position_dodge

can plot common violin, one sample

Code
  p$data
Output
                        sgRNA gene         sample values
  1 A1BG_CACCTTCGAGCTGCTGCGCG A1BG HELA_T15A_CTRL    519
  2 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG HELA_T15A_CTRL      0
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG HELA_T15A_CTRL    193

Code
  p$layers
Output
  [[1]]
  geom_violin: draw_quantiles = NULL, na.rm = FALSE, orientation = NA
  stat_ydensity: trim = TRUE, scale = area, na.rm = FALSE, orientation = NA
  position_dodge

can plot density ridges, all samples

Code
  p$data
Output
                         sgRNA gene         sample values
  1  A1BG_CACCTTCGAGCTGCTGCGCG A1BG        HELA_T0    478
  2  A1BG_AAGAGCGCCTCGGTCCCAGC A1BG        HELA_T0      0
  3  A1BG_TGGACTTCCAGCTACGGCGC A1BG        HELA_T0    274
  4  A1BG_CACCTTCGAGCTGCTGCGCG A1BG HELA_T15A_CTRL    519
  5  A1BG_AAGAGCGCCTCGGTCCCAGC A1BG HELA_T15A_CTRL      0
  6  A1BG_TGGACTTCCAGCTACGGCGC A1BG HELA_T15A_CTRL    193
  7  A1BG_CACCTTCGAGCTGCTGCGCG A1BG HELA_T15B_CTRL    439
  8  A1BG_AAGAGCGCCTCGGTCCCAGC A1BG HELA_T15B_CTRL      0
  9  A1BG_TGGACTTCCAGCTACGGCGC A1BG HELA_T15B_CTRL    163
  10 A1BG_CACCTTCGAGCTGCTGCGCG A1BG HELA_T15C_CTRL    587
  11 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG HELA_T15C_CTRL     52
  12 A1BG_TGGACTTCCAGCTACGGCGC A1BG HELA_T15C_CTRL    161
  13 A1BG_CACCTTCGAGCTGCTGCGCG A1BG  HELA_T15A_OLA    389
  14 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG  HELA_T15A_OLA      0
  15 A1BG_TGGACTTCCAGCTACGGCGC A1BG  HELA_T15A_OLA     80
  16 A1BG_CACCTTCGAGCTGCTGCGCG A1BG  HELA_T15B_OLA    591
  17 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG  HELA_T15B_OLA     16
  18 A1BG_TGGACTTCCAGCTACGGCGC A1BG  HELA_T15B_OLA    393
  19 A1BG_CACCTTCGAGCTGCTGCGCG A1BG  HELA_T15C_OLA    274
  20 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG  HELA_T15C_OLA      0
  21 A1BG_TGGACTTCCAGCTACGGCGC A1BG  HELA_T15C_OLA     45

Code
  p$layers
Output
  [[1]]
  geom_density_ridges: na.rm = FALSE, panel_scaling = TRUE
  stat_density_ridges: na.rm = FALSE
  position_points_sina

can plot common density ridges, with groups

Code
  p$data
Output
                         sgRNA gene         sample values          group
  1  A1BG_CACCTTCGAGCTGCTGCGCG A1BG        HELA_T0    478        HELA_T0
  2  A1BG_AAGAGCGCCTCGGTCCCAGC A1BG        HELA_T0      0        HELA_T0
  3  A1BG_TGGACTTCCAGCTACGGCGC A1BG        HELA_T0    274        HELA_T0
  4  A1BG_CACCTTCGAGCTGCTGCGCG A1BG HELA_T15A_CTRL    519 HELA_T15A_CTRL
  5  A1BG_AAGAGCGCCTCGGTCCCAGC A1BG HELA_T15A_CTRL      0 HELA_T15A_CTRL
  6  A1BG_TGGACTTCCAGCTACGGCGC A1BG HELA_T15A_CTRL    193 HELA_T15A_CTRL
  7  A1BG_CACCTTCGAGCTGCTGCGCG A1BG HELA_T15B_CTRL    439 HELA_T15B_CTRL
  8  A1BG_AAGAGCGCCTCGGTCCCAGC A1BG HELA_T15B_CTRL      0 HELA_T15B_CTRL
  9  A1BG_TGGACTTCCAGCTACGGCGC A1BG HELA_T15B_CTRL    163 HELA_T15B_CTRL
  10 A1BG_CACCTTCGAGCTGCTGCGCG A1BG HELA_T15C_CTRL    587 HELA_T15C_CTRL
  11 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG HELA_T15C_CTRL     52 HELA_T15C_CTRL
  12 A1BG_TGGACTTCCAGCTACGGCGC A1BG HELA_T15C_CTRL    161 HELA_T15C_CTRL
  13 A1BG_CACCTTCGAGCTGCTGCGCG A1BG  HELA_T15A_OLA    389  HELA_T15A_OLA
  14 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG  HELA_T15A_OLA      0  HELA_T15A_OLA
  15 A1BG_TGGACTTCCAGCTACGGCGC A1BG  HELA_T15A_OLA     80  HELA_T15A_OLA
  16 A1BG_CACCTTCGAGCTGCTGCGCG A1BG  HELA_T15B_OLA    591  HELA_T15B_OLA
  17 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG  HELA_T15B_OLA     16  HELA_T15B_OLA
  18 A1BG_TGGACTTCCAGCTACGGCGC A1BG  HELA_T15B_OLA    393  HELA_T15B_OLA
  19 A1BG_CACCTTCGAGCTGCTGCGCG A1BG  HELA_T15C_OLA    274  HELA_T15C_OLA
  20 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG  HELA_T15C_OLA      0  HELA_T15C_OLA
  21 A1BG_TGGACTTCCAGCTACGGCGC A1BG  HELA_T15C_OLA     45  HELA_T15C_OLA

Code
  p$layers
Output
  [[1]]
  geom_density_ridges: na.rm = FALSE, panel_scaling = TRUE
  stat_density_ridges: na.rm = FALSE
  position_points_sina

can plot common density ridges, one sample

Code
  p$data
Output
                        sgRNA gene         sample values
  1 A1BG_CACCTTCGAGCTGCTGCGCG A1BG HELA_T15A_CTRL    519
  2 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG HELA_T15A_CTRL      0
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG HELA_T15A_CTRL    193

Code
  p$layers
Output
  [[1]]
  geom_density_ridges: na.rm = FALSE, panel_scaling = TRUE
  stat_density_ridges: na.rm = FALSE
  position_points_sina

cancerit/RCRISPR documentation built on April 26, 2023, 10:12 p.m.