Package platetools. R topics documented: June 25, Title Tools and Plots for Multi-Well Plates Version 0.1.1

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1 Title Tools and Plots for Multi-Well Plates Version Package platetools June 25, 2018 Collection of functions for working with multi- microtitre plates, mainly 96, 384 and 1536 plates. Depends R (>= 3.1.0) License MIT + file LICENSE URL BugReports Encoding UTF-8 LazyData true Imports dplyr, plyr, RColorBrewer, ggplot2 Suggests testthat, viridis RoxygenNote NeedsCompilation no Author Scott Warchal [aut, cre] Maintainer Scott Warchal <s.warchal@sms.ed.ac.uk> Repository CRAN Date/Publication :03:45 UTC R topics documented: bhit_map b_grid b_map b_score check_plate_input dist_map fill_plate hit_grid hit_map

2 2 bhit_map is_ list_to_frame med_smooth missing_s num_to_ pchit_grid pchit_map pc_grid pc_map plate_effect plate_map plate_map_grid plate_map_grid_scale plate_map_multiple plate_map_scale plate_matrix plt plt plt raw_grid raw_map readmap_ read_map rotate_plate set_block _to_num z_grid z_map Index 27 bhit_map Platemap to identify hits following a B-score normalisation Produces a platemap with colours indicating s above or below selected threshold after normalising for systematic plate effects via B-score smooth. The threshold is definined calculated from a z-score, i.e plus or minus standard deviations from the plate mean. bhit_map(,, plate = 96, threshold = 2, palette = "Spectral")

3 b_grid 3 Vector of numerical values Vector of identifiers, e.g "A01" plate Number of s in whole plate (96, 384 or 1536) threshold Standard deviations from the plate average to indicate a hit. default is set to +/- 2 SD. palette ggplot plot RColorBrewer palette df <-.frame(vals = rnorm(384), = num_to_(1:384, plate = 384)) bhit_map( = df$vals, = df$, plate = 384, threshold = 3) b_grid Plots multiple b-scored normalised platemaps Transforms numerical values using the b-score normalisation process to account for row and column effects. Uses and plate labels to plot the normalised values in the form of microtitre plates. Works for 96, 384 and 1536 plates. b_grid(,, plate_id, plate = 96) plate_id Numerical values to be plotted Vector of identifiers e.g "A01" Vector of plate identifiers e.g "Plate_1" plate Number of s in complete plate (96, 384 or 1536) ggplot plot

4 4 b_map df01 <-.frame( = num_to_(1:96), vals = rnorm(96), plate = 1) df02 <-.frame( = num_to_(1:96), vals = rnorm(96), plate = 2) df <- rbind(df01, df02) b_grid( = df$vals, = df$, plate_id = df$plate, plate = 96) b_map Plots a heatmap of b-score normalised values in a plate layout Transforms numerical values using the b-score normalisation process to account for row and column effects. Uses labels to plot the normalised values in the form of a microtitre plate. Works for 96, 384 or 1536 plates b_map(,, normalise = FALSE, plate = 96) normalise Numerical values in the form of a vector to be normalised Vector of identifiers, e.g "A01" Not currently used plate integer, 96, 384 or 1536 ggplot plot df <-.frame( = num_to_(1:96), vals = rnorm(96)) b_map( = df$vals, = df$, plate = 96)

5 b_score 5 df_384 <-.frame( = num_to_(1:384, plate = 384), vals = rnorm(384)) b_map( = df_384$vals, = df_384$, plate = 384) b_score 2 way median polish 2 way median polish to remove plate effects such as row/column/edge effects. Given a frame containing alpha-numeric IDs and numerical values, this b_score will return a frame of the same structure after a two-way median smooth. b_score(,, plate) numeric, either a vector or frame column alpha-numeric IDs. e.g A01 plate numeric, number of s within a plate, either 96 or 384 df <-.frame( = num_to_(1:96), vals = rnorm(96)) b_score( = df$vals, = df$, plate = 96)

6 6 dist_map check_plate_input checks plate input for dodgy plate combinations checks plate input for dodgy plate combinations check_plate_input(, plate) plate vector of labels integer, number of s in full plate dist_map Plots distributions per in a plate layout Produces distribution plots facetted in a plate-layout format. dist_map(, ) vector of alphanumeric IDs e.g A01 numeric vector ggplot plot

7 fill_plate 7 fill_plate Fill in missing s Fills in missing s with rows of NA values. Useful for any functions that require a complete plate such as b_score. fill_plate(df,, plate = 96) df frame Column containing identifiers i.e "A01" plate Number of s in complete plate (96, 384 or 1536) frame vals <- rnorm(96) ; s <- num_to_(1:96) df <-.frame(s, vals) df_missing <- df[-c(1:10), ] fill_plate(df_missing, "s") hit_grid Plots multiple platemaps with and identifies hits Converts numerical values and labels into hits in the form of multiple plate maps. Hits are calculated as s above or below a specified number of standard deviations from the overall average hit_grid(,, plate_id, threshold = 2, ncols = 2, plate = 96, each = FALSE, palette = "Spectral")

8 8 hit_map plate_id threshold ncols Numerical values to be scaled and plotted Vector of identifiers. e.g "A01" Vector of plate identifiers e.g "Plate_1" Numerical value of standard deviations from the mean for a to be classified as a hit. Default it +/- 2 SD Number of columns in the grid of plates plate Number of s in the complete plates (96, 384 or 1536) each palette ggplot plot boolean, if true scales each plate individually, if false will scale the pooled values of RColorBrewer palette df01 <-.frame( = num_to_(1:96), vals = rnorm(96), plate = 1) df02 <-.frame( = num_to_(1:96), vals = rnorm(96), plate = 2) df <- rbind(df01, df02) hit_grid( = df$vals, = df$, plate_id = df$plate, plate = 96, each = FALSE) hit_map Platemap to identify hits in a screen Produces a plot in the form of a micro-titre layout, with colours indicating s above or below a nominated threshold. hit_map(,, plate = 96, threshold = 2, palette = "Spectral")

9 is_ Vector of numerical values to score Vector of identifiers e.g "A01" plate Number of s in complete plate (96, 384 or 1536) threshold palette Numerical value of standard deviations from the mean for a to be classified as a hit. Default it +/- 2 SD RColorBrewer palette ggplot plot df <-.frame(vals = rnorm(1:384), = num_to_(1:384, plate = 384)) hit_map( = df$vals, = df$, plate = 384, threshold = 3) is_1536 internal 1536 plate function for plate_map internal 1536 plate function for plate_map is_1536() vector of alphanumeric labels

10 10 med_smooth list_to_frame Converts list to a frame in a sensible way Given a list of frames with the same columns, this function will row bind them together, and if passed a col_name arguement, will produce a column containing their original element name list_to_frame(l, col_name = NULL) l col_name list of frames to be converted into single frame (optional) name of column to put element names under frame med_smooth 2-way median smooth Given a platemap produced by plate_map, will return a frame with after values have been transformed into a matrix mirroring the plate structure and undergoing a 2-way median polish to remove row or column effects med_smooth(platemap, plate) platemap frame produced by plate_map plate numeric, number of s in plate, either 96 or 384 A frame consisting of two column, ID and polished numeric values

11 missing_s 11 missing_s Returns s that are missing from a complete plate Returns a vector of s that are missing from a complete plate. missing_s(df,, plate = 96) df frame Column containing identifiers i.e "A01" plate Number of s in complete plate (96 or 384) vector of missing s vals <- rnorm(96) ; s <- num_to_(1:96) df <-.frame(vals, s) df_missing <- df[-c(1:10), ] missing_s(df_missing, "s") num_to_ Converts numbers to labels Converts numerical values to corresponding alpha-numeric labels for 96, 384 or 1536 plates. num_to_(x, plate = 96) x Vector of numbers to be converted plate Number of s in complete plate (96 or 384)

12 12 pchit_grid Vector of alpha-numeric labels num_to_(1:96) num_to_(1:96, plate = 384) nums <- c(1:10, 20:40, 60:96) num_to_(nums) pchit_grid Plots multiple heatmaps identifying hits from the first principal component Converts numerical values, labels, and plate labels into multiple heatmaps of plates, with z- scored principal components coloured dependent on a specified threshold of standard deviations above or below the average. pchit_grid(,, plate_id,...) plate_id Numerical values, either a frame or a matrix Vector of identifers e.g "A01" Vector of plate identifiers e.g "Plate_1"... additional arguments to platetools::hit_grid() ggplot plot df01 <-.frame( = num_to_(1:96), plate = 1, vals1 = rnorm(1:96), vals2 = rnorm(1:96)) df02 <-.frame( = num_to_(1:96), plate = 2, vals1 = rnorm(1:96),

13 pchit_map 13 vals2 = rnorm(1:96)) df <- rbind(df01, df02) pchit_grid( = df[,3:4], = df$, plate_id = df$plate, plate = 96) pchit_map Plots a heatmap identifying hits from the first principal component Converts numerical values and plate labels intoa plate heatmap with z-scored principal components coloured dependent on a specified threshold of standard deviations above or below the average. pchit_map(,, plate = 96, threshold = 2, palette = "Spectral") Numerical values, either a frame or a matrix Vector of identifers e.g "A01" plate Number of s in complete plate (96, 384 or 1536) threshold Threshold of +/- standard deviations form the average to determine a hit palette RColorBrewer palette ggplot plot v1 <- rnorm(1:96) v2 <- rnorm(1:96) v3 <- rnorm(1:96) s <- num_to_(1:96) df <-.frame(s, v1, v2, v3) pchit_map( = df[, 2:4], = df$s, threshold = 1.5)

14 14 pc_grid pc_grid Plots multiple platemaps as a heatmap of the first principal component. Converts multivariate and labels into a heatmap of the first principal component in the form of a grid of platemaps. pc_grid(,, plate_id, ncols = 2, plate = 96,...) plate_id ncols Numerical values be transformed, scaled and plotted as a colour Vector of identifiers e.g "A01" Vector of plate labels or identifiers e.g "plate_1" Number of columns to plot multiple platemaps plate Number of s in complete plate (96, 384 or 1536)... additional arguments to be passed to z_grid ggplot plot df01 <-.frame( = num_to_(1:96), plate = 1, vals1 = rnorm(1:96), vals2 = rnorm(1:96)) df02 <-.frame( = num_to_(1:96), plate = 2, vals1 = rnorm(1:96), vals2 = rnorm(1:96)) df <- rbind(df01, df02) pc_grid( = df[, 3:4], = df$, plate_id = df$plate, plate = 96)

15 pc_map 15 pc_map Principal component heatmap in a plate layout Takes the values and identifiers, calculates the first principal component, scales and plots the component as a heatmap in the form of a 96 or 384- plate. A way to quickly show variation of multi-parametric within a plate. pc_map(,, plate = 96) Vector of numerical to calculate the first principal component Vector of identifiers e.g "A01" plate Number of s in complete plate (96, 384 or 1536 gplot plot df <-.frame( = num_to_(1:96), vals1 = rnorm(1:96), vals2 = rnorm(1:96)) pc_map( = df[, 2:3], = df$, plate = 96) plate_effect Two way-median smooth on a plate map Given a platemap produced by plate_map, this will perform a two way median smooth, and return the results of medpolish. Useful for row and column effects, as as the raw residuals. plate_effect(platemap, plate)

16 16 plate_map_grid platemap platemap produced by plate_map plate, integer either 96 or 384 plate_map creates frame of row,column, from ID and internal function plate_map(, ) numeric to be used as colour scale alpha-numeric IDs, e.g A01 frame plate_map_grid creates frame of row, column, plate_id from regarding IDs internal function plate_map_grid(,, plate_id) plate_id numerical to be used as colour scale alpha-numeric IDs, e.g A01 plate identifers e.g plate_1 frame

17 plate_map_grid_scale 17 plate_map_grid_scale creates frame of row, column, plate_id from regarding IDs internal function plate_map_grid_scale(,, plate_id, each) plate_id each numerical to be used as colour scale alpha-numeric IDs, e.g A01 plate identifers e.g plate_1 boolean, if true scales each plate individually, if false will scale the pooled values of frame plate_map_multiple row, column for multiple features Generates a frame for multiple features, given a ID column and multiple features plate_map_multiple(, ) vector or frame of numeric vector of alphanumeric IDs e.g A01

18 18 plate_matrix plate_map_scale creates frame of row, column, and scaled from IDs internal function plate_map_scale(, ) numeric to be used as colour scale alpha-numeric IDs, e.g A01 frame plate_matrix plate layout matrix from IDs Given a frame of alpha-numeric IDs e.g ("A01"), and values, this function will produce a matrix in the form of a plate layout. plate_matrix(,, plate = 96) vector of to be placed in matrix vector of alphanumeric IDs. e.g ("A01") plate number of s in plate (96 or 384) matrix

19 plt a <- 1:96 s <- num_to_(1:96) plate_matrix( = a, = s) x <- rnorm(384) s <- num_to_(1:384, plate = 384) plate_matrix( = x, = s, plate = 384) plt1536 ggplot plate object internal function plt1536(platemap) platemap platemap frame produced by plate_map ggplot object plt384 ggplot plate object internal function plt384(platemap) platemap platemap frame produced by plate_map ggplot object

20 20 raw_grid plt96 ggplot plate object internal function plt96(platemap) platemap platemap frame produced by plate_map ggplot object raw_grid Plots multiple platemaps with heatmap of raw values Converts numerical values. labels, and plate labels into multiple plate heatmaps raw_grid(,, plate_id, ncols = 2, plate = 96) Numerical values to be plotted Vector of identifiers e.g "A01" plate_id Vector of plate identifiers e.g "Plate_1" ncols Number of columns to display multiple heatmaps plate Number of s in complete plate (96, 384 or 1536) ggplot plot

21 raw_map 21 df01 <-.frame( = num_to_(1:96), vals = rnorm(96), plate = 1) df02 <-.frame( = num_to_(1:96), vals = rnorm(96), plate = 2) df <- rbind(df01, df02) raw_grid( = df$vals, = df$, plate_id = df$plate, plate = 96) raw_map Plots a platemap with heatmap of raw values Converts numerical values and labels into multiple plate heatmaps raw_map(,, plate = 96) Numerical values to be plotted Vector of identifiers e.g "A01" plate Number of s in complete plate (96, 384 or 1536) ggplot plot df <-.frame(vals = rnorm(1:384), = num_to_(1:384, plate = 384)) raw_map( = df$vals, = df$, plate = 384)

22 22 read_map readmap_ example in a plate map form example in a plate map form readmap_ Format 96 integers structured in a the form of a 96- plate Source none read_map Annotates frame with meta in a platemap matrix Annotates a frame containined identifiers with meta in the form of a platemap matrix, matching the existing -labels to the position in the platemap read_map(, map, verbose = TRUE, new_col_name = "header") map verbose new_col_name existing daatframe, with IDs under the column name of Matrix of meta to be added to the frame, N.B NO MISSING WELLS! Boolean, if TRUE will add row and column numbers to frame What to call the added meta frame with new column named after new_col_name

23 rotate_plate 23 rotate_plate rotates matrix by 180 degrees If someone (no names) puts in a plate upside down, this function will rotate a plate matrix produced by plate_matrix to be the correct way up. I.e if A01 is in the bottom right hand corner rather than the top left. rotate_plate(m) m matrix matrix set_block Set values in rectangular areas of a plate Updates a table representing a multi plate, by setting a given value for all s in a block or a list of blocks defined by the coordinates of their upper-left and bottom-right corners. set_block(plate, block, what, value) plate block what value A table representing a multi plate, with one column named representing the identifiers. Coordinates of a rectangular block (such as A01~B02 ), or a vector of coordinates. A column name in the table. The value to set. Details This function is tested with a table in.frame format, but it should also work with the DataFrame,.table and tibble formats.

24 24 _to_num Returns the plate table, where the values for the s indicated in the blocks have been updated. Author(s) Charles Plessy See Also num_to_ p <-.frame( = num_to_(1:96)) head(p) p <- set_block(p, c("a01~b02", "A05~D05"), "dntp", 0.25) p <- set_block(p, "A03", "dntp", 0.50) head(p) # Be careful with the column names p <- set_block(p, "A01~H12", "Mg2+", 3.0) head(p) ## Not run: # Chained updates with magrittr p %<>% setblock("a01~c04", "dntp", 0.5) %>% setblock("a01~c04", "Mg", 3.0) ## End(Not run) _to_num Converts labels to numbers Converts alpha-numeric labels to numbers corresponding to positions within a microtitre plate. Either 96 or 384 plate, in column-wise order or in a column snaking pattern. _to_num(s, style = "normal", plate = 96)

25 z_grid 25 s style Vector of identifiers e.g "A01" Either normal, starting at the left hand column at each row or in a snaking fashion. ( normal or snake ) plate Number of s in the complete plate (96 or 384) Vector of numbers _to_num("a01") _to_num("p12", plate = 384) _to_num("p12", plate = 384, style = "snake") s <- c("a01", "A02", "A03") _to_num(s) z_grid Plots multiple platemaps with heatmap of scaled values Converts numerical values. labels, and plate labels into multiple plate heatmaps z_grid(,, plate_id, ncols = 2, plate = 96, each = FALSE) plate_id ncols Numerical values to be plotted Vector of identifiers e.g "A01" Vector of plate identifiers e.g "Plate_1" Number of columns to display multiple heatmaps plate Number of s in complete plate (96, 384 or 1569) each ggplot plot boolean, if true scales each plate individually, if false will scale the pooled values of

26 26 z_map df01 <-.frame( = num_to_(1:96), vals = rnorm(96), plate = 1) df02 <-.frame( = num_to_(1:96), vals = rnorm(96), plate = 2) df <- rbind(df01, df02) z_grid( = df$vals, = df$, plate_id = df$plate, plate = 96) z_map Plots a platemap with heatmap of scaled values Converts numerical values and labels into multiple plate heatmaps z_map(,, plate = 96) Numerical values to be plotted Vector of identifiers e.g "A01" plate Number of s in complete plate (96, 384 or 1536)) ggplot plot df <-.frame(vals = rnorm(1:384), = num_to_(1:384, plate = 384)) z_map( = df$vals, = df$, plate = 384)

27 Index Topic sets readmap_, 22 b_grid, 3 b_map, 4 b_score, 5 bhit_map, 2 check_plate_input, 6.frame, 23.table, 23 DataFrame, 23 dist_map, 6 fill_plate, 7 hit_grid, 7 hit_map, 8 plt384, 19 plt96, 20 raw_grid, 20 raw_map, 21 read_map, 22 readmap_, 22 rotate_plate, 23 set_block, 23 tibble, 23 _to_num, 24 z_grid, 25 z_map, 26 is_1536, 9 list_to_frame, 10 med_smooth, 10 missing_s, 11 num_to_, 11, 24 pc_grid, 14 pc_map, 15 pchit_grid, 12 pchit_map, 13 plate_effect, 15 plate_map, 16 plate_map_grid, 16 plate_map_grid_scale, 17 plate_map_multiple, 17 plate_map_scale, 18 plate_matrix, 18 plt1536, 19 27